MolNFT v1 · #169489 · protein

Structure of human HDAC2 in complex with an aryl ketone inhibitor

6XDM: “Structure of human HDAC2 in complex with an aryl ketone inhibitor”. X-ray diffraction, 4 ligands (V1D, CA, ZN). MolNFT v1 #169489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XDM
Type: protein
Length: 1,101 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q92769
Ligands: V1D, CA, ZN, SO4

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	368	—	Q92769
B	—	protein	367	—	Q92769
C	—	protein	366	—	Q92769

Ligands and binding sites

V1D · N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide · ligand · 3 copies · chains A, B, C
CA · Calcium ion · metal · 6 copies · chains A, B, C
ZN · Zinc ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

6XDM · Structure of human HDAC2 in complex with an aryl ketone inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q92769 · AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q92769
Elsewhere: RCSB PDB 6XDM · PDBe 6XDM · UniProt Q92769

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