2C5V

Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug Design

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2c5va_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cyclin-dependent PK, CDK2	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2c5vc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cyclin-dependent PK, CDK2	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2c5vd1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	Cyclin A	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2c5vb1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	Cyclin A	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040310	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040310	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyclin-like	8038665	3000768	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyclin-like	8038664	3000768	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8038665	3000768	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8038664	3000768	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	Pkinase_Tyr	e2c5vA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
C	Pkinase_Tyr	e2c5vC1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
D	Cyclin_C	e2c5vD2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_C	ECOD (1.6)
D	Cyclin_N	e2c5vD1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N	ECOD (1.6)
B	Cyclin_C	e2c5vB2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_C	ECOD (1.6)
B	Cyclin_N	e2c5vB1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
B	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
B, D	PF02984	Cyclin, C-terminal domain (Cyclin_C)	Cyclin, C-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the C-terminal domain.	Domain
B, D	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	CELL DIVISION PROTEIN KINASE 2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity cyclin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein binding protein domain specific binding cyclin binding protein serine kinase activity cation binding magnesium ion binding metal ion 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 cell division microtubule organizing center organization microtubule cytoskeleton organization centrosome duplication centrosome cycle microtubule-based process cell cycle cytoskeleton organization cell cycle process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process DNA replication positive regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition cellular senescence centriole assembly organelle assembly membraneless organelle assembly cellular component biogenesis cellular component assembly centriole replication macromolecule modification protein metabolic process post-translational protein modification protein modification process protein phosphorylation phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process DNA repair cell cycle G2/M phase transition regulation of G2/M transition of mitotic cell cycle G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to nitric oxide cellular response to chemical stimulus response to chemical response to nitric oxide cellular response to reactive nitrogen species regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication initiation small GTPase-mediated signal transduction Ras protein signal transduction intracellular signaling cassette localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process catabolic process regulation of anaphase-promoting complex-dependent catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process sexual reproduction reproductive process meiotic cell cycle positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of heterochromatin formation chromatin organization positive regulation of chromatin organization chromatin remodeling regulation of heterochromatin formation regulation of chromatin organization heterochromatin formation positive regulation of cellular component biogenesis epigenetic regulation of gene expression regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of chromosome organization negative regulation of gene expression negative regulation of gene expression, epigenetic	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol transcription regulator complex sex chromosome membraneless organelle intracellular membraneless organelle chromosome X chromosome Cajal body membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen Y chromosome cyclin E2-CDK2 complex male germ cell nucleus germ cell nucleus chromosome, telomeric region chromosomal region cyclin A2-CDK2 complex condensed chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cyclin E1-CDK2 complex endosome intracellular vesicle cytoplasmic vesicle vesicle cyclin A1-CDK2 complex
B, D	CYCLIN A2	protein binding binding protein domain specific binding kinase binding enzyme binding protein kinase binding enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development cellular response to stimulus cellular response to nitrogen compound response to stimulus cellular response to gonadotropin stimulus cellular response to luteinizing hormone stimulus response to endogenous stimulus response to luteinizing hormone developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development cellular response to stimulus cellular response to nitrogen compound response to stimulus cellular response to gonadotropin stimulus cellular response to luteinizing hormone stimulus response to endogenous stimulus response to luteinizing hormone response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to gonadotropin cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular process cellular response to hormone stimulus cellular response to insulin-like growth factor stimulus cellular response to growth factor stimulus cellular response to platelet-derived growth factor stimulus response to growth factor response to platelet-derived growth factor cell division response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus response to glucagon regulation of biological process regulation of cellular process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process fibroblast proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of cellular process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process small GTPase-mediated signal transduction signaling Ras protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction macromolecule modification protein metabolic process post-translational protein modification protein modification process cellular response to leptin stimulus response to leptin cellular response to organic cyclic compound response to alkaloid cellular response to cocaine cellular response to alkaloid response to organic cyclic compound response to cocaine mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription response to lipid cellular response to lipid response to estradiol cellular response to estradiol stimulus regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA metabolic process DNA biosynthetic process animal organ regeneration regeneration cell cycle G2/M phase transition G2/M transition of mitotic cell cycle cellular response to nitric oxide response to nitric oxide cellular response to reactive nitrogen species	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pronucleus male pronucleus female pronucleus cyclin A2-CDK1 complex cyclin A2-CDK2 complex
E [auth F], F [auth H]	ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000719	Protein kinase domain	Domain
A, C	IPR050108	Cyclin-dependent kinase	Family
A, C	IPR017441	Protein kinase, ATP binding site	Binding Site
A, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, D	IPR048258	Cyclins, cyclin-box	Conserved Site
B, D	IPR004367	Cyclin, C-terminal domain	Domain
B, D	IPR032447	Cyclin-A, N-terminal APC/C binding region	Domain
B, D	IPR046965	Cyclin A/B-like	Family
B, D	IPR006671	Cyclin, N-terminal	Domain
B, D	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B, D	IPR039361	Cyclin	Family
B, D	IPR013763	Cyclin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P24941	melanoma glioblastoma large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma adrenal cortex carcinoma primitive neuroectodermal tumor alopecia areata vitiligo atypical teratoid rhabdoid tumor Childhood Diffuse Large B-Cell Lymphoma diffuse large B-cell lymphoma malignant colon neoplasm pilocytic astrocytoma melanoma glioblastoma large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma adrenal cortex carcinoma primitive neuroectodermal tumor alopecia areata vitiligo atypical teratoid rhabdoid tumor Childhood Diffuse Large B-Cell Lymphoma diffuse large B-cell lymphoma malignant colon neoplasm pilocytic astrocytoma psoriasis asthma breast disease cleft lip eye disease Hashimoto thyroiditis hypothyroidism malignant ependymoma malignant mesothelioma polycystic ovary syndrome allergic rhinitis rheumatoid arthritis attention deficit hyperactivity disorder, inattentive type cancer cutaneous melanoma gastroesophageal reflux disease hematologic disease
B, D	Pharos: P20248	intellectual disability psoriasis Liver Cirrhosis, Experimental malignant ependymoma medulloblastoma nasopharyngeal carcinoma ovarian cancer peripheral nervous system disease adrenal cortex carcinoma breast cancer Sjogren syndrome Crohn disease endometriosis large cell medulloblastoma lung cancer intellectual disability psoriasis Liver Cirrhosis, Experimental malignant ependymoma medulloblastoma nasopharyngeal carcinoma ovarian cancer peripheral nervous system disease adrenal cortex carcinoma breast cancer Sjogren syndrome Crohn disease endometriosis large cell medulloblastoma lung cancer malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy atopic eczema breast carcinoma tuberculosis cutaneous lupus erythematosus eye disease interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor atypical teratoid rhabdoid tumor schizophrenia cancer ulcerative colitis ductal breast carcinoma in situ glioblastoma invasive ductal breast carcinoma lung adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth F], F [auth H]	ABA	Parent Component: ALA RESID: AA0253 , AA0409 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819
E [auth F], F [auth H]	NH2	RESID: AA0253 , AA0409 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109
E [auth F], F [auth H]	PFF	Parent Component: PHE RESID: AA0253 , AA0409 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.