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Structure of PDB 6fyz Chain C Binding Site BS01

Receptor Information
>6fyz Chain C (length=349) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSTKPRFTTGLVYDTLMLKHQCTCSHPEHAGRIQSIWSRLQETGLRGKCE
CIRGRKATLEELQTVHSEAHTLLYGTNPLNTIWNEVHSAGAARLAVGCVV
ELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRL
SVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDE
VGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLV
SSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLT
AICDASEACVSALLGNEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRH
Ligand information
Ligand IDEBE
InChIInChI=1S/C19H16FN3O2/c1-12-21-10-15(11-22-12)13-6-8-14(9-7-13)18(19(24)23-25)16-4-2-3-5-17(16)20/h2-11,18,25H,1H3,(H,23,24)/t18-/m0/s1
InChIKeySFXMVIQZYOMYOF-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(cn1)c2ccc(cc2)[C@H](C(=O)NO)c3ccccc3F
OpenEye OEToolkits 2.0.6Cc1ncc(cn1)c2ccc(cc2)[C@@H](c3ccccc3F)C(=O)NO
OpenEye OEToolkits 2.0.6Cc1ncc(cn1)c2ccc(cc2)C(c3ccccc3F)C(=O)NO
CACTVS 3.385Cc1ncc(cn1)c2ccc(cc2)[CH](C(=O)NO)c3ccccc3F
FormulaC19 H16 F N3 O2
Name(2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide
ChEMBL
DrugBank
ZINC
PDB chain6fyz Chain C Residue 2001 [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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PDB6fyz Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		P676 E677 H802 H803 G811 F812 D840 H842 F871 P942 L943 G974
Binding residue
(residue number reindexed from 1)		P27 E28 H123 H124 G132 F133 D161 H163 F192 P263 L264 G295
Annotation score1
Binding affinityMOAD: Kd=0.039uM
BindingDB: IC50=36nM,Kd=80nM
Enzymatic activity
Enzyme Commision number 3.5.1.98: histone deacetylase.
External links
PDB RCSB:6fyz, PDBe:6fyz, PDBj:6fyz
PDBsum6fyz
PubMed30463802
UniProtP56524|HDAC4_HUMAN Histone deacetylase 4 (Gene Name=HDAC4)

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