SMTL ID : 7ltl.3 (2 other biounits)

STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR LACKING A ZINC BINDING GROUP (COMPOUND 19)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: ACT.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265, ACT.9

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 1 residues within 4Å: Chain A: R.230 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.358, A:K.362 Salt bridges: A:R.230, A:K.362 SO4.3: 5 residues within 4Å: Chain A: Y.304, T.305, I.306, R.307, Y.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.306, A:R.307 Water bridges: A:R.307 Salt bridges: A:R.307 SO4.4: 2 residues within 4Å: Chain A: K.67, K.166 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.166 Salt bridges: A:K.67, A:K.166 SO4.5: 2 residues within 4Å: Chain A: H.58, K.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.59 Water bridges: A:K.59 Salt bridges: A:H.58 SO4.6: 2 residues within 4Å: Chain A: R.213, R.366 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.213, A:R.366

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:T.191, A:V.194, H2O.4, H2O.8 CA.8: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.177, A:H.179, A:S.198, A:F.199

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 11 residues within 4Å: Chain A: H.141, H.142, G.150, C.152, D.177, H.179, D.265, G.302, Y.304 Ligands: ZN.1, YEV.11 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.141, A:H.142, A:H.179

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

PEG.10: 5 residues within 4Å: Chain A: L.165, K.166, Y.167, Q.169, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.169

1 x YEV: (2R)-2-(5-hydroxy-2-methyl-1H-indol-3-yl)-N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}propanamide(Non-covalent)

YEV.11: 15 residues within 4Å: Chain A: G.28, H.29, P.30, D.100, G.150, F.151, H.179, E.204, Y.205, F.206, P.207, G.208, L.272, Y.304 Ligands: ACT.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.151, A:F.151, A:F.206, A:F.206, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:D.100 Water bridges: A:Y.205, A:F.206 pi-Stacking: A:F.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beshore, D.C. et al., Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction. Acs Med.Chem.Lett. (2021)

Release Date

2021-05-05

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 2

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