SMTL ID : 4lxz.1 (2 other biounits)

Structure of Human HDAC2 in complex with SAHA (vorinostat)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.170, H.172, D.258, G.295 Ligands: SHH.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.170, A:D.170, A:H.172, A:D.258

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.168, D.170, H.172, S.191, F.192, H.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.168, A:D.168, A:D.170, A:H.172, A:S.191

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: F.181, T.184, V.187, Y.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.216

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 8 residues within 4Å: Chain A: K.60, K.138, L.155, L.158, A.180, F.181, T.184, R.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.138, A:R.186 PG4.5: 4 residues within 4Å: Chain A: R.300, E.329, Y.330, G.332 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.300 PG4.6: 4 residues within 4Å: Chain A: D.12, N.15, Y.16, D.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.15

1 x SHH: OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE(Non-covalent)

SHH.7: 15 residues within 4Å: Chain A: G.21, H.22, P.23, D.93, H.134, H.135, G.143, F.144, D.170, H.172, F.199, D.258, G.295, Y.297 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.144, A:F.144, A:F.144, A:F.144, A:F.199 Hydrogen bonds: A:D.93, A:H.135, A:Y.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lauffer, B.E. et al., Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability. J.Biol.Chem. (2013)

Release Date

2013-08-21

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 2

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