SMTL ID : 5wgm.3 (2 other biounits)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ACY-1083

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: AH7.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.178, A:H.180, A:S.199, A:L.200 K.3: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:D.192, A:V.195, A:Y.228, H2O.4

1 x AH7: 2-[(4,4-difluoro-1-phenylcyclohexyl)amino]-N-hydroxypyrimidine-5-carboxamide(Non-covalent)

AH7.4: 15 residues within 4Å: Chain A: H.29, P.30, S.97, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.1, EDO.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.209, A:L.278 Hydrogen bonds: A:S.97, A:S.97, A:Y.311 pi-Stacking: A:F.149, A:H.180, A:F.209

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 8 residues within 4Å: Chain A: S.6, S.7, P.8, I.9, G.125, Q.126, V.127, R.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.6, A:I.9, A:I.9 Water bridges: A:S.6 EDO.6: 4 residues within 4Å: Chain A: Q.34, S.37, R.38, S.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.37, A:S.41 EDO.7: 6 residues within 4Å: Chain A: H.22, M.24, L.88, S.101, N.102, E.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.102, A:N.102 EDO.8: 3 residues within 4Å: Chain A: Y.14, F.40, R.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.54, A:R.54 Water bridges: A:Q.16 EDO.9: 2 residues within 4Å: Chain A: R.42, L.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.42, A:R.42 EDO.10: 3 residues within 4Å: Chain A: M.19, L.20, P.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.19 EDO.11: 4 residues within 4Å: Chain A: A.66, L.67, C.68, H.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.69 Water bridges: A:L.67, A:R.160 EDO.12: 4 residues within 4Å: Chain A: R.202, E.204, G.236, G.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.202, A:G.236, A:G.237 Water bridges: A:G.237 EDO.13: 5 residues within 4Å: Chain A: N.96, F.209, P.210, N.211 Ligands: AH7.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.210 EDO.14: 4 residues within 4Å: Chain A: M.245, H.290, S.334, L.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.335 Water bridges: A:S.334 EDO.15: 5 residues within 4Å: Chain A: R.274, P.285, T.314, S.315, E.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.274, A:S.315

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 6 residues within 4Å: Chain A: P.8, I.9, T.10, R.51, L.327, L.328 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.10, A:R.51 Water bridges: A:S.50

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 5 residues within 4Å: Chain A: R.171, D.193, Y.228, E.258, F.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.193 Water bridges: A:R.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-12-06

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Hdac6 protein

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