Structure of PDB 7kbg Chain B

Receptor sequence

>7kbgB (length=366) Species: 9606 (Homo sapiens)

KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHK
ATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFE
FCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVL
AILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT
GDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVV
LQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNV
ARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEY
MEKIKQRLFENLRMLP

3D structure

• PDB: 7kbg Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group.
• Chain: B
• Resolution: 1.26 Å

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	D168 H170 D256
BS02	CA	B	D175 D177 H179 S198 F199	D166 D168 H170 S189 F190
BS03	CA	B	F188 T191 V194 Y223	F179 T182 V185 Y214
BS04	WBA	B	G28 H29 P30 M31 E99 D100 G139 H141 H142 G150 F151 C152 D177 H179 F206 G301 G302 Y304	G19 H20 P21 M22 E90 D91 G130 H132 H133 G141 F142 C143 D168 H170 F197 G292 G293 Y295	MOAD: ic50=29nM

Gene Ontology

Molecular Function

• GO:0004407 histone deacetylase activity

External links

• PDB: RCSB:7kbg, PDBe:7kbg, PDBj:7kbg
• PDBsum: 7kbg
• PubMed: 33335670
• UniProt: Q92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)