Structure of PDB 6xdm Chain B

Receptor sequence
>6xdmB (length=367) Species: 9606 (Homo sapiens) [Search protein sequence]
KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPH
KATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLF
EFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIV
LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPG
TGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAV
VLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRN
VARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPE
YMEKIKQRLFENLRMLP
3D structure
PDB6xdm Selective Class I HDAC Inhibitors Based on Aryl Ketone Zinc Binding Induce HIV-1 Protein for Clearance.
ChainB
Resolution1.56 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN B D177 H179 D265 D169 H171 D257
BS02 CA B D175 D177 H179 S198 F199 D167 D169 H171 S190 F191
BS03 CA B F188 T191 V194 Y223 F180 T183 V186 Y215
BS04 V1D B P30 M31 D100 H141 H142 G150 F151 C152 H179 F206 G301 G302 Y304 P22 M23 D92 H133 H134 G142 F143 C144 H171 F198 G293 G294 Y296 MOAD: ic50=0.1nM
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity

View graph for
Molecular Function
External links
PDB RCSB:6xdm, PDBe:6xdm, PDBj:6xdm
PDBsum6xdm
PubMed32676157
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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