Structure of PDB 6xdm Chain A

Receptor sequence
>6xdmA (length=368) Species: 9606 (Homo sapiens) [Search protein sequence]
GKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRP
HKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGL
FEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDI
VLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFP
GTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSA
VVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIR
NVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTP
EYMEKIKQRLFENLRMLP
3D structure
PDB6xdm Selective Class I HDAC Inhibitors Based on Aryl Ketone Zinc Binding Induce HIV-1 Protein for Clearance.
ChainA
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 A D177 H179 D265 D170 H172 D258
BS02 CA A D175 D177 H179 S198 F199 D168 D170 H172 S191 F192
BS03 CA A F188 V194 Y223 F181 V187 Y216
BS04 V1D A P30 M31 D100 L140 H141 H142 G150 F151 C152 H179 F206 G302 Y304 P23 M24 D93 L133 H134 H135 G143 F144 C145 H172 F199 G295 Y297 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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