6WS5 | pdb_00006ws5

Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth HHH]	SCOP2B Superfamily	DNA repair protein REV1 C-terminal domain-like	8091495	3002514	SCOP2B (2022-06-29)
B [auth CCC]	SCOP2B Superfamily	HORMA/p31comet-like	8058134	3000150	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth HHH]	F_UNCLASSIFIED	e6ws5HHH1	A: alpha superhelices	X: Repetitive alpha hairpins	H: DNA repair protein Rev1 C-terminal domain (From Topology)	T: DNA repair protein Rev1 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth CCC]	HORMA	e6ws5CCC1	A: a+b two layers	X: The spindle assembly checkpoint protein mad2 (From Topology)	H: The spindle assembly checkpoint protein mad2 (From Topology)	T: The spindle assembly checkpoint protein mad2	F: HORMA	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth HHH]	PF16727	DNA repair protein REV1 C-terminal domain (REV1_C)	DNA repair protein REV1 C-terminal domain	This is the C-terminal domain of DNA repair protein REV1. It interacts with REV7, POLN, POLK and POLI [1-2].	Domain
B [auth CCC]	PF02301	HORMA domain (HORMA)	HORMA domain	The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle ...	The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth HHH]	DNA repair protein REV1	deoxycytidyl transferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid DNA binding binding damaged DNA binding nucleic acid binding cation binding deoxycytidyl transferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid DNA binding binding damaged DNA binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response response to stress error-prone translesion synthesis DNA biosynthetic process DNA repair response to light stimulus response to radiation response to abiotic stimulus response to UV error-free translesion synthesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
B [auth CCC]	Mitotic spindle assembly checkpoint protein MAD2B	JUN kinase binding protein binding binding kinase binding enzyme binding protein kinase binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding	cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization cellular response to stress DNA damage response response to stress cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization cellular response to stress DNA damage response response to stress cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination regulation of response to stimulus negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response immune response immune effector process regulation of gene expression biosynthetic process positive regulation of DNA metabolic process B cell mediated immunity positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process immunoglobulin production regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination positive regulation of lymphocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments positive regulation of biosynthetic process regulation of immunoglobulin mediated immune response positive regulation of isotype switching regulation of B cell activation leukocyte activation involved in immune response positive regulation of immune effector process positive regulation of cellular process positive regulation of immunoglobulin production production of molecular mediator of immune response regulation of isotype switching cell activation macromolecule biosynthetic process positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation multicellular organismal process regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity cell activation involved in immune response positive regulation of developmental process positive regulation of cell activation positive regulation of metabolic process positive regulation of leukocyte activation anatomical structure development leukocyte mediated immunity somatic diversification of immune receptors positive regulation of adaptive immune response positive regulation of immune system process somatic recombination of immunoglobulin genes involved in immune response developmental process positive regulation of nucleobase-containing compound metabolic process regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins regulation of leukocyte mediated immunity positive regulation of multicellular organismal process regulation of immune response regulation of production of molecular mediator of immune response isotype switching immune system development positive regulation of lymphocyte mediated immunity immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of biological process lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process B cell activation gene expression positive regulation of B cell activation adaptive immune response immunoglobulin mediated immune response regulation of immunoglobulin production regulation of lymphocyte mediated immunity regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion mediated by cadherin cell-cell adhesion mediated by cadherin negative regulation of cell-cell adhesion regulation of cell-cell adhesion regulation of cell-cell adhesion mediated by cadherin negative regulation of DNA-binding transcription factor activity RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process negative regulation of molecular function nucleobase-containing compound biosynthetic process regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription cell division positive regulation of DNA repair regulation of double-strand break repair via nonhomologous end joining positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining positive regulation of double-strand break repair regulation of epithelial to mesenchymal transition cellular developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of cell differentiation cell differentiation animal organ development tissue development epithelial to mesenchymal transition mesenchymal cell differentiation regulation of cellular component organization positive regulation of cellular component organization positive regulation of cellular component biogenesis positive regulation of extracellular matrix organization extracellular matrix organization regulation of cellular component biogenesis cellular component biogenesis cellular component assembly regulation of extracellular matrix assembly positive regulation of extracellular matrix assembly regulation of extracellular matrix organization extracellular matrix assembly extracellular structure organization external encapsulating structure organization regulation of cell cycle phase transition spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction cell cycle mitotic sister chromatid separation chromosome segregation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling negative regulation of cellular component organization regulation of cell cycle process sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation mitotic cell cycle process regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle signaling spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle regulation of mitotic cell cycle mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition regulation of cell cycle negative regulation of chromosome separation cell cycle process mitotic nuclear division negative regulation of mitotic cell cycle phase transition organelle fission negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling nuclear division negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of cell communication regulation of growth growth regulation of cell growth cell growth positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation DNA damage response, signal transduction resulting in transcription signal transduction in response to DNA damage negative regulation of RNA biosynthetic process negative regulation of DNA-templated transcription negative regulation of transcription by competitive promoter binding negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process translesion synthesis postreplication repair DNA synthesis involved in DNA repair error-prone translesion synthesis DNA biosynthetic process negative regulation of cell differentiation negative regulation of developmental process negative regulation of epithelial to mesenchymal transition negative regulation of multicellular organismal process regulation of DNA binding regulation of binding negative regulation of binding negative regulation of transcription regulatory region DNA binding regulation of transcription regulatory region DNA binding negative regulation of DNA binding positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process catabolic process macromolecule catabolic process negative regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of catabolic process protein catabolic process regulation of catabolic process regulation of protein catabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II negative regulation of post-translational protein modification negative regulation of ubiquitin protein ligase activity regulation of catalytic activity regulation of protein ubiquitination negative regulation of catalytic activity regulation of transferase activity regulation of ubiquitin protein ligase activity negative regulation of ubiquitin-protein transferase activity protein ubiquitination negative regulation of transferase activity negative regulation of protein modification process regulation of ubiquitin-protein transferase activity negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex cytoskeleton spindle microtubule cytoskeleton site of double-strand break site of DNA damage
C [auth ZZZ]	DNA polymerase zeta catalytic subunit	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding ion binding metal ion binding	translesion synthesis cellular response to stimulus postreplication repair response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response translesion synthesis cellular response to stimulus postreplication repair response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response response to stress metabolic process cellular process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA repair double-strand break repair DNA recombination recombinational repair double-strand break repair via homologous recombination DNA-templated DNA replication DNA replication	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth HHH]	IPR047346	DNA repair protein REV1, ubiquitin-binding motif 1/2	Conserved Site
A [auth HHH]	IPR031991	DNA repair protein Rev1, C-terminal	Domain
A [auth HHH]	IPR001126	UmuC domain	Domain
A [auth HHH]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth HHH]	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
A [auth HHH]	IPR012112	DNA repair protein Rev1	Family
A [auth HHH]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A [auth HHH]	IPR025527	HUWE1/REV1, ubiquitin-binding motif	Conserved Site
A [auth HHH]	IPR038401	Rev1, C-terminal domain superfamily	Homologous Superfamily
A [auth HHH]	IPR001357	BRCT domain	Domain
A [auth HHH]	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
A [auth HHH]	IPR053848	DNA polymerase IV/DNA polymerase iota-like, thumb domain	Domain
A [auth HHH]	IPR036420	BRCT domain superfamily	Homologous Superfamily
B [auth CCC]	IPR045091	Mad2-like	Family
B [auth CCC]	IPR036570	HORMA domain superfamily	Homologous Superfamily
B [auth CCC]	IPR003511	HORMA domain	Domain
C [auth ZZZ]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth ZZZ]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
C [auth ZZZ]	IPR006172	DNA-directed DNA polymerase, family B	Family
C [auth ZZZ]	IPR025687	C4-type zinc-finger of DNA polymerase delta	Domain
C [auth ZZZ]	IPR030559	DNA polymerase zeta catalytic subunit	Family
C [auth ZZZ]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth ZZZ]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
C [auth ZZZ]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
C [auth ZZZ]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
C [auth ZZZ]	IPR032757	Domain of unknown function DUF4683	Domain
C [auth ZZZ]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth ZZZ]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth HHH]	Pharos: Q9UBZ9	attention deficit hyperactivity disorder, inattentive type osteosarcoma pancreatic intraductal papillary-mucinous neoplasm xeroderma pigmentosum brucellosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia large cell medulloblastoma pancreatic intraductal papillary-mucinous carcinoma rheumatoid arthritis
B [auth CCC]	Pharos: Q9UI95	Fanconi anemia Fanconi anemia complementation group V aplastic anemia glioblastoma malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma hematopoietic and lymphoid system neoplasm malignant glioma pancreatic intraductal papillary-mucinous neoplasm inherited aplastic anemia medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
C [auth ZZZ]	Pharos: O60673	Mobius syndrome psoriasis attention deficit hyperactivity disorder, inattentive type glioblastoma juvenile dermatomyositis medulloblastoma osteosarcoma primitive neuroectodermal tumor skin disease Crohn disease inflammatory bowel disease lung adenocarcinoma ovarian cancer ulcerative colitis dermatomyositis Mobius syndrome psoriasis attention deficit hyperactivity disorder, inattentive type glioblastoma juvenile dermatomyositis medulloblastoma osteosarcoma primitive neuroectodermal tumor skin disease Crohn disease inflammatory bowel disease lung adenocarcinoma ovarian cancer ulcerative colitis dermatomyositis invasive ductal breast carcinoma malignant ependymoma myopathy pilocytic astrocytoma psoriatic arthritis