SMTL ID : 6tcy.1 (1 other biounit)

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS555

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.173, H.175, D.266 Ligands: N28.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:D.173, A:H.175, A:D.266, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.171, D.173, H.175, S.194, L.195, H.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.173, A:H.175, A:S.194, A:L.195 K.3: 4 residues within 4Å: Chain A: F.184, D.187, V.190, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.184, A:V.190, A:Y.223, H2O.3, H2O.8

1 x N28: 4-[[[4-(aminomethyl)phenyl]carbamoyl-(4-oxidanylbutyl)amino]methyl]-~{N}-oxidanyl-benzamide(Non-covalent)

N28.4: 16 residues within 4Å: Chain A: D.21, P.25, S.92, H.134, H.135, G.143, F.144, D.173, H.175, F.204, D.266, L.273, G.304, Y.306 Ligands: ZN.1, TOE.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.25, A:F.204, A:F.204, A:L.273 Hydrogen bonds: A:H.135 Water bridges: A:D.21, A:D.21 pi-Stacking: A:F.144, A:H.175

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

EDO.5: 6 residues within 4Å: Chain A: L.118, T.161, R.162, L.165, E.257, R.297 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.162, A:E.257, A:R.297 EDO.6: 7 residues within 4Å: Chain A: Q.181, E.185, K.214, V.215, G.216, L.217, N.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.215, A:G.216 Water bridges: A:Q.181 EDO.7: 4 residues within 4Å: Chain A: E.281, P.328, S.329, L.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.329 Water bridges: A:E.281 EDO.8: 2 residues within 4Å: Chain A: E.40, R.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.42, A:R.42 EDO.9: 3 residues within 4Å: Chain A: R.37, E.40, L.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.37, A:R.37

1 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.10: 8 residues within 4Å: Chain A: N.18, D.21, H.24, S.92, I.93, F.94, F.144 Ligands: N28.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18, A:D.21, A:D.21

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain A: R.162, R.166, E.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 Water bridges: A:R.162

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: E.39, R.42, L.44, S.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noonepalle, S. et al., Rational Design of Suprastat: A Novel Selective Histone Deacetylase 6 Inhibitor with the Ability to Potentiate Immunotherapy in Melanoma Models. J.Med.Chem. (2020)

Release Date

2020-11-04

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Histone deacetylase 6

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