Structure of PDB 6g3o Chain A Binding Site BS03

Receptor Information
>6g3o Chain A (length=369) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYR
PHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDG
LFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVND
IVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYF
PGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPS
AVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTI
RNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNT
PEYMEKIKQRLFENLRMLP
Ligand information
Ligand IDEL8
InChIInChI=1S/C18H20F3N3O5/c1-10(4-2-3-5-13(25)24-28)22-14-15(17(27)16(14)26)23-11-6-8-12(9-7-11)29-18(19,20)21/h6-10,22-23,28H,2-5H2,1H3,(H,24,25)/t10-/m1/s1
InChIKeyWFKNHSZTAURQLQ-SNVBAGLBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](CCCCC(=O)NO)NC1=C(Nc2ccc(OC(F)(F)F)cc2)C(=O)C1=O
OpenEye OEToolkits 2.0.6C[C@H](CCCCC(=O)NO)NC1=C(C(=O)C1=O)Nc2ccc(cc2)OC(F)(F)F
OpenEye OEToolkits 2.0.6CC(CCCCC(=O)NO)NC1=C(C(=O)C1=O)Nc2ccc(cc2)OC(F)(F)F
CACTVS 3.385C[C@H](CCCCC(=O)NO)NC1=C(Nc2ccc(OC(F)(F)F)cc2)C(=O)C1=O
FormulaC18 H20 F3 N3 O5
Name(6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide
ChEMBLCHEMBL4242292
DrugBank
ZINC
PDB chain6g3o Chain A Residue 1004 [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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PDB6g3o Squaramides as novel class I and IIB histone deacetylase inhibitors for topical treatment of cutaneous t-cell lymphoma.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		G32 H33 P34 D104 H145 H146 G154 F155 D181 H183 F210 L276 Y308
Binding residue
(residue number reindexed from 1)		G22 H23 P24 D94 H135 H136 G144 F145 D171 H173 F200 L266 Y298
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.24,Ki=0.58nM
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:6g3o, PDBe:6g3o, PDBj:6g3o
PDBsum6g3o
PubMed30122227
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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