Structure of PDB 7ltg Chain B Binding Site BS04

Receptor Information
>7ltg Chain B (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHK
ATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFE
FCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVL
AILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT
GDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVV
LQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNV
ARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEY
MEKIKQRLFENLRML
Ligand information
Ligand IDYED
InChIInChI=1S/C34H51N5O7/c1-5-22(3)29-33(43)38-19-13-11-17-28(38)32(42)35-25(15-8-7-12-18-34(44,45)6-2)30(40)36-26(31(41)37-29)20-23-21-39(46-4)27-16-10-9-14-24(23)27/h9-10,14,16,21-22,25-26,28-29,44-45H,5-8,11-13,15,17-20H2,1-4H3,(H,35,42)(H,36,40)(H,37,41)/t22-,25-,26-,28+,29-/m0/s1
InChIKeyYTTBRMMMZWYPGH-WLUNDFKZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC(C)C1C(=O)N2CCCCC2C(=O)NC(C(=O)NC(C(=O)N1)Cc3cn(c4c3cccc4)OC)CCCCCC(CC)(O)O
CACTVS 3.385CC[CH](C)[CH]1NC(=O)[CH](Cc2cn(OC)c3ccccc23)NC(=O)[CH](CCCCCC(O)(O)CC)NC(=O)[CH]4CCCCN4C1=O
CACTVS 3.385CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2cn(OC)c3ccccc23)NC(=O)[C@H](CCCCCC(O)(O)CC)NC(=O)[C@H]4CCCCN4C1=O
OpenEye OEToolkits 2.0.7CC[C@H](C)[C@H]1C(=O)N2CCCC[C@@H]2C(=O)N[C@H](C(=O)N[C@H](C(=O)N1)Cc3cn(c4c3cccc4)OC)CCCCCC(CC)(O)O
ACDLabs 12.01O=C1C(NC(C(NC(C2N(C(C(N1)C(C)CC)=O)CCCC2)=O)CCCCCC(CC)(O)O)=O)Cc3c4c(n(c3)OC)cccc4
FormulaC34 H51 N5 O7
Name(3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone
ChEMBL
DrugBank
ZINC
PDB chain7ltg Chain B Residue 409 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7ltg Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
G28 H29 P30 D100 H141 H142 G150 F151 D177 H179 F206 R271 G302 Y304
Binding residue
(residue number reindexed from 1)
G19 H20 P21 D91 H132 H133 G141 F142 D168 H170 F197 R262 G293 Y295
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity

View graph for
Molecular Function
External links
PDB RCSB:7ltg, PDBe:7ltg, PDBj:7ltg
PDBsum7ltg
PubMed33854701
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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