SMTL ID : 5wgk.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HPB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

11 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 1 residues within 4Å: Chain A: W.25 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: H.29, S.97 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: L.298, A.299 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: K.84, P.85, R.86 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: L.278 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: M.245, A.246, H.249 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: P.277, N.312 Ligand excluded by PLIP IOD.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: S.79 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: G.223, R.226 Ligand excluded by PLIP IOD.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: AGJ.16 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

3 x K: POTASSIUM ION(Non-covalent)

K.13: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.14: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.3, H2O.7 K.15: 4 residues within 4Å: Chain A: K.219, V.220, G.221, L.222 No protein-ligand interaction detected (PLIP)

1 x AGJ: N-hydroxy-4-{[(2-hydroxyethyl)(phenylacetyl)amino]methyl}benzamide(Non-covalent)

AGJ.16: 14 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.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.209, A:L.278 Hydrogen bonds: A:D.271, A:Y.311 Water bridges: A:D.178, A:D.178 pi-Stacking: A:F.149

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

EDO.17: 3 residues within 4Å: Chain A: Q.34, R.38, L.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.38 Water bridges: A:S.37, A:S.37 EDO.18: 2 residues within 4Å: Chain A: R.54, P.56 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain A: R.17, A.57, R.58, L.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17, A:R.17 Water bridges: A:A.57, A:L.59, A:L.59 EDO.20: 4 residues within 4Å: Chain A: P.8, I.9, R.51, L.328 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.51 Water bridges: A:T.10, A:T.10, A:L.328, A:D.330 EDO.21: 2 residues within 4Å: Chain A: Q.120, T.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.120 EDO.22: 3 residues within 4Å: Chain A: S.41, E.44, E.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 EDO.23: 5 residues within 4Å: Chain A: R.274, P.285, T.314, S.315, E.318 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.274, A:S.315 Water bridges: A:E.318 EDO.24: 6 residues within 4Å: Chain A: H.53, R.54, I.55, P.56, A.121, Q.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.126 EDO.25: 5 residues within 4Å: Chain A: D.241, P.242, L.335, L.338, T.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.338, A:T.339, A:T.339 EDO.26: 6 residues within 4Å: Chain A: H.250, L.341, T.346, I.349, N.350, L.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.350 Water bridges: A:N.350 EDO.27: 3 residues within 4Å: Chain A: N.89, R.90, D.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.93, A:D.93 EDO.28: 1 residues within 4Å: Chain A: K.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.72, A:K.72 EDO.29: 5 residues within 4Å: Chain A: D.193, G.223, K.224, R.226, Y.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.193 EDO.30: 4 residues within 4Å: Chain A: L.46, L.48, M.322, S.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.325 Water bridges: A:L.46, A:L.46, A:R.51

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

PEG.31: 5 residues within 4Å: Chain A: Y.14, D.15, Q.16, F.40, R.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.15, A:Q.16, A:R.54, A:R.54 Water bridges: A:Q.16

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
A

Hdac6 protein

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