RCSB PDB: Search

3GV4 \| pdb_00003gv4	Download File View File

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG

Dong, A., Ravichandran, M., Loppnau, P., Li, Y., MacKenzie, F., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Dhe-Paganon, S., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

To be published

Released	2009-04-28
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein) ubiquitin C-terminal peptide RLRGG (protein)
Unique Ligands	CA, ZN

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3PHD \| pdb_00003phd	Download File View File

Crystal structure of human HDAC6 in complex with ubiquitin

Dong, A., Qui, W., Ravichandran, M., Schuetz, A., Loppnau, P., Li, F., Mackenzie, F., Kozieradzki, I., Ouyang, H., Structural Genomics Consortium (SGC)

(2012) J Biological Chem 287: 2317-2327

Released	2011-02-23
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein) Polyubiquitin (protein)
Unique Ligands	ZN

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5B8D \| pdb_00005b8d	Download File View File

Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Tempel, W., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., Ravichandran, M., Schapira, M., Bountra, C., Edwards, A.M., von Delft, F., Santhakumar, V., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2017) J Med Chem 60: 9090-9096

Released	2016-07-27
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	6T4, FMT, NA, UNX, ZN

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5EDU \| pdb_00005edu	Download File View File

Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A

Hai, Y., Christianson, D.W.

(2016) Nat Chem Biol 12: 741-747

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Maltose-binding periplasmic protein, Histone deacetylase 6 chimera (protein)
Unique Ligands	K, TSN, ZN
Unique branched monosaccharides	GLC

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5KH3 \| pdb_00005kh3	Download File View File

Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Dong, A., Ravichandran, M., Ferreira de Freitas, R., Schapira, M., Bountra, C., Edwards, A.M., Santhakumar, V., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2017) J Med Chem 60: 9090-9096

Released	2016-07-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	6U6, UNX, ZN

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5KH7 \| pdb_00005kh7	Download File View File

Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Walker, J., Ravichandran, M., Ferreira de Freitas, R., Schapira, M., Bountra, C., Edwards, A.M., Santhakumar, V., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2017) J Med Chem 60: 9090-9096

Released	2016-07-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	6T7, UNX, ZN

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5KH9 \| pdb_00005kh9	Download File View File

Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Tempel, W., Ravichandran, M., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., Schapira, M., Bountra, C., Edwards, A.M., von Delft, F., Santhakumar, V., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2017) J Med Chem 60: 9090-9096

Released	2016-07-27
Method	X-RAY DIFFRACTION 1.07 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	6T5, FMT, NA, UNX, ZN

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5WBN \| pdb_00005wbn	Download File View File

Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Walker, J.R., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H.

To be published

Released	2017-08-02
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	9ZV, ACT, CL, FMT, UNX, ZN

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5WPB \| pdb_00005wpb	Download File View File

Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Tempel, W., Ferreira de Freitas, R., Franzoni, I., Ravichandran, M., Lautens, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

(2017) J Med Chem 60: 9090-9096

Released	2017-08-23
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	B8P, UNX, ZN

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6CE6 \| pdb_00006ce6	Download File View File

Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EYP, UNX, ZN

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6CE8 \| pdb_00006ce8	Download File View File

Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EYV, UNX, ZN

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6CEA \| pdb_00006cea	Download File View File

Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EYY, UNX, ZN

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6CEC \| pdb_00006cec	Download File View File

Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Franzoni, I., Ravichandran, M., Lautens, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EY7, UNX, ZN

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6CED \| pdb_00006ced	Download File View File

Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Franzoni, I., Ravichandran, M., Lautens, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EYA, UNX, ZN

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6CEE \| pdb_00006cee	Download File View File

Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Franzoni, I., Ravichandran, M., Lautens, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EYM, UNX, ZN

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6CEF \| pdb_00006cef	Download File View File

Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Halabelian, L., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 4517-4527

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	EYJ, UNX, ZN

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7ZYU \| pdb_00007zyu	Download File View File

HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10

Wang, L., Kempf, G.

(2022) Cell Rep 39: 110736-110736

Released	2022-06-01
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Designed Ankyrin repeat protein F10 (protein) Histone deacetylase 6 (protein)
Unique Ligands	EDO, ZN

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8G43 \| pdb_00008g43	Download File View File

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid

Harding, R.J., Franzoni, I., Mann, M.K., Szewczyk, M., Mirabi, B., Owens, D.D.G., Ackloo, S., Scheremetjew, A., Juarez-Ornelas, K.A., Sanichar, R., Baker, R.J., Dank, C., Brown, P.J., Barsyte-Lovejoy, D., Santhakumar, V., Schapira, M., Lautens, M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

(2023) J Med Chem 66: 10273-10288

Released	2023-05-03
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	ZN, ZU6

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8G44 \| pdb_00008g44	Download File View File

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(benzylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid

Harding, R.J., Franzoni, I., Mann, M.K., Szewczyk, M., Mirabi, B., Owens, D.D.G., Ackloo, S., Scheremetjew, A., Juarez-Ornelas, K.A., Sanichar, R., Baker, R.J., Dank, C., Brown, P.J., Barsyte-Lovejoy, D., Santhakumar, V., Schapira, M., Lautens, M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

(2023) J Med Chem 66: 10273-10288

Released	2023-05-03
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	ZN, ZU9

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8G45 \| pdb_00008g45	Download File View File

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe

Harding, R.J., Franzoni, I., Mann, M.K., Szewczyk, M., Mirabi, B., Owens, D.D.G., Ackloo, S., Scheremetjew, A., Juarez-Ornelas, K.A., Sanichar, R., Baker, R.J., Dank, C., Brown, P.J., Barsyte-Lovejoy, D., Santhakumar, V., Schapira, M., Lautens, M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

(2023) J Med Chem 66: 10273-10288

Released	2023-05-03
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 6 (protein)
Unique Ligands	ZN, ZUE

3GV4 | pdb_00003gv4

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG

3PHD | pdb_00003phd

Crystal structure of human HDAC6 in complex with ubiquitin

5B8D | pdb_00005b8d

Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain

5EDU | pdb_00005edu

Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A

5KH3 | pdb_00005kh3

Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

5KH7 | pdb_00005kh7

Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

5KH9 | pdb_00005kh9

Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

5WBN | pdb_00005wbn

Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

5WPB | pdb_00005wpb

Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

6CE6 | pdb_00006ce6

Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid

6CE8 | pdb_00006ce8

Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

6CEA | pdb_00006cea

Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

6CEC | pdb_00006cec

Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

6CED | pdb_00006ced

Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

6CEE | pdb_00006cee

Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

6CEF | pdb_00006cef

Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

7ZYU | pdb_00007zyu

HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10

8G43 | pdb_00008g43

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid

8G44 | pdb_00008g44

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(benzylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid

8G45 | pdb_00008g45

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe

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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

3GV4 | pdb_00003gv4

3PHD | pdb_00003phd

5B8D | pdb_00005b8d

5EDU | pdb_00005edu

5KH3 | pdb_00005kh3

5KH7 | pdb_00005kh7

5KH9 | pdb_00005kh9

5WBN | pdb_00005wbn

5WPB | pdb_00005wpb

6CE6 | pdb_00006ce6

6CE8 | pdb_00006ce8

6CEA | pdb_00006cea

6CEC | pdb_00006cec

6CED | pdb_00006ced

6CEE | pdb_00006cee

6CEF | pdb_00006cef

7ZYU | pdb_00007zyu

8G43 | pdb_00008g43

8G44 | pdb_00008g44

8G45 | pdb_00008g45