RCSB PDB: Search

2V5W \| pdb_00002v5w	Download File View File

Crystal structure of HDAC8-substrate complex

Di Marco, S., Vannini, A., Volpari, C.

(2007) EMBO Rep 8: 879

Released	2007-09-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	GLYCYL-GLYCYL-GLYCINE (protein) HISTONE DEACETYLASE 8 (protein) PEPTIDIC SUBSTRATE (protein)
Unique Ligands	K, ZN

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2V5X \| pdb_00002v5x	Download File View File

Crystal structure of HDAC8-inhibitor complex

Di Marco, S., Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfi, A., Defrancesco, R., Steinkuhler, C.

(2007) EMBO Rep 8: 879

Released	2007-09-04
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 8 (protein)
Unique Ligands	K, V5X, ZN

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2VQJ \| pdb_00002vqj	Download File View File

Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	DIO, K, SO4, TFG, ZN

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2VQM \| pdb_00002vqm	Download File View File

Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	HA3, K, ZN

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2VQO \| pdb_00002vqo	Download File View File

Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a trifluoromethylketone inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	K, SO4, TFG, ZN

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2VQQ \| pdb_00002vqq	Download File View File

Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	K, SO4, TFG, ZN

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2VQV \| pdb_00002vqv	Download File View File

Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-22
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	HA3, K, SO4, ZN

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2VQW \| pdb_00002vqw	Download File View File

Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr)

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-08-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	K, ZN

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3O0U \| pdb_00003o0u	Download File View File

Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG

Fradera, X., van Zeeland, M., Uitdehaag, J.C.M.

(2010) Bioorg Med Chem Lett 20: 6237-6241

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Cathepsin K (protein)
Unique Ligands	O47

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3O1G \| pdb_00003o1g	Download File View File

Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group.

Fradera, X., van Zeeland, M., Uitdehaag, J.C.M.

(2010) Bioorg Med Chem Lett 20: 6237-6241

Released	2010-10-06
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Cathepsin K (protein)
Unique Ligands	O75, SO4

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4TT2 \| pdb_00004tt2	Download File View File

Crystal structure of ATAD2A bromodomain complexed with H4(1-20)K5Ac peptide

Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

(2015) Biochem J 466: 337-346

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	ATPase family AAA domain-containing protein 2 (protein) Histone H4K5Ac (protein)

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4TT4 \| pdb_00004tt4	Download File View File

Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K14Ac peptide

Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

(2015) Biochem J 466: 337-346

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	ATPase family AAA domain-containing protein 2 (protein) Histone H3(1-21)K4Ac (protein)
Unique Ligands	CL, SO4

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4TT6 \| pdb_00004tt6	Download File View File

Crystal structure of ATAD2A bromodomain double mutant N1063A-Y1064A in apo form

Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

(2015) Biochem J 466: 337-346

Released	2014-12-24
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	ATPase family AAA domain-containing protein 2 (protein)
Unique Ligands	CL, GOL, SO4

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4TTE \| pdb_00004tte	Download File View File

Crystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate

Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

(2015) Biochem J 466: 337-346

Released	2014-12-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	ATPase family AAA domain-containing protein 2 (protein)
Unique Ligands	36Z, CL, GOL, SO4

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4TU4 \| pdb_00004tu4	Download File View File

Crystal structure of ATAD2A bromodomain complexed with 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(phenylsulfonyl)amino]benzoicacid

Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

(2015) Biochem J 466: 337-346

Released	2014-12-24
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Homo sapiens
Macromolecule	ATPase family AAA domain-containing protein 2 (protein)
Unique Ligands	37N, CL, DMS, GOL, SO4

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4TU6 \| pdb_00004tu6	Download File View File

Crystal structure of apo ATAD2A bromodomain with N1064 alternate conformation

Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

(2015) Biochem J 466: 337-346

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Homo sapiens
Macromolecule	ATPase family AAA domain-containing protein 2 (protein)
Unique Ligands	SO4

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4UZM \| pdb_00004uzm	Download File View File

Shotgun proteolysis: A practical application

Allen, M.D., Bycroft, M., Freund, S.M.V., Christ, D.

(2015) Protein Eng Des Sel 28: 445

Released	2014-09-17
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PUTATIVE MEMBRANE PROTEIN IGAA HOMOLOG (protein)

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4YAB \| pdb_00004yab	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with 1-methyl-5-(2-methyl-1 3-thiazol-4-yl)-2 3-dihydro-1H-indol-2-one (1)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4CN, SO4, ZN

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4YAD \| pdb_00004yad	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with 2,4-dimethoxy-N-(1-methyl-2-oxo-1,2,3,4-tetrahydroquinolin-6-yl)benzene-1-sulfonamide (3b)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4A7, CL, GOL, ZN

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4YAT \| pdb_00004yat	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with N-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-4-methoxybenzene-1-sulfonamide (5b)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4A8, ZN

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4YAX \| pdb_00004yax	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with N-[6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl]benzenesulfonamide (5g)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4AE, GOL, SO4, ZN

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4YBM \| pdb_00004ybm	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with N-{6-[3-(benzyloxy)phenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide (7b)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.46 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4BJ, GOL, SO4, ZN

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4YBS \| pdb_00004ybs	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with N-{1,3-dimethyl-6-[3-(2-methylpropoxy)phenoxy]-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-1,2-dimethyl-1H-imidazole-4-sulfonamide (7g)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4BK, DMS, ZN

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4YBT \| pdb_00004ybt	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with N-{1,3-dimethyl-2-oxo-6-[3-(oxolan-3-ylmethoxy)phenoxy]-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-1-methyl-1H-imidazole-4-sulfonamide (7l)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4BV, DMS, ZN

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4YC9 \| pdb_00004yc9	Download File View File

Crystal structure of TRIM24 PHD-bromodomain complexed with N-(6-{3-[4-(dimethylamino)butoxy]-5-propoxyphenoxy}-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-3,4-dimethoxybenzene-1-sulfonamide (8i)

Poncet-Montange, G., Palmer, W., Jones, P.

(2016) J Med Chem 59: 1440-1454

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Homo sapiens
Macromolecule	Transcription intermediary factor 1-alpha (protein)
Unique Ligands	4C1, GOL, ZN

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2V5W | pdb_00002v5w

2V5X | pdb_00002v5x

2VQJ | pdb_00002vqj

2VQM | pdb_00002vqm

2VQO | pdb_00002vqo

2VQQ | pdb_00002vqq

2VQV | pdb_00002vqv

2VQW | pdb_00002vqw

3O0U | pdb_00003o0u

3O1G | pdb_00003o1g

4TT2 | pdb_00004tt2

4TT4 | pdb_00004tt4

4TT6 | pdb_00004tt6

4TTE | pdb_00004tte

4TU4 | pdb_00004tu4

4TU6 | pdb_00004tu6

4UZM | pdb_00004uzm

4YAB | pdb_00004yab

4YAD | pdb_00004yad

4YAT | pdb_00004yat

4YAX | pdb_00004yax

4YBM | pdb_00004ybm

4YBS | pdb_00004ybs

4YBT | pdb_00004ybt

4YC9 | pdb_00004yc9