Structure of PDB 2vcg Chain D Binding Site BS04

Receptor Information
>2vcg Chain D (length=375) Species: 512 (Alcaligenes sp.) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHHHHHHAIGYVWNTLYGWVDTGTGSLAAANLTARMQPISHHLAHPDTKR
RFHELVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGG
DTGDGITMMGNGGLEIARLSAGGAVELTRRVATGELSAGYALVNPPGHHA
PHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWND
PSVLTISLHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHA
MDQVVLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTID
CAADICDGRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAG
MGGNTLLDAERAAIEEIVPLLADIR
Ligand information
Ligand IDS17
InChIInChI=1S/C18H25BrN2O5/c1-26-18(24)15(12-13-8-10-14(19)11-9-13)20-16(22)6-4-2-3-5-7-17(23)21-25/h8-11,15,25H,2-7,12H2,1H3,(H,20,22)(H,21,23)/t15-/m0/s1
InChIKeyUPYGSQPRAHMDPD-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COC(=O)C(Cc1ccc(cc1)Br)NC(=O)CCCCCCC(=O)NO
CACTVS 3.341COC(=O)[CH](Cc1ccc(Br)cc1)NC(=O)CCCCCCC(=O)NO
ACDLabs 10.04Brc1ccc(cc1)CC(C(=O)OC)NC(=O)CCCCCCC(=O)NO
OpenEye OEToolkits 1.5.0COC(=O)[C@H](Cc1ccc(cc1)Br)NC(=O)CCCCCCC(=O)NO
CACTVS 3.341COC(=O)[C@H](Cc1ccc(Br)cc1)NC(=O)CCCCCCC(=O)NO
FormulaC18 H25 Br N2 O5
Namemethyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate
ChEMBLCHEMBL406734
DrugBankDB08505
ZINCZINC000016052595
PDB chain2vcg Chain D Residue 1381 [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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PDB2vcg Phenylalanine-Containing Hydroxamic Acids as Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs).
Resolution1.9 Å
Binding residue
(original residue number in PDB)		L27 I106 H148 H149 F158 D186 H188 F214 Y318
Binding residue
(residue number reindexed from 1)		L27 I106 H148 H149 F158 D186 H188 F214 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.77,IC50=1.69uM
Enzymatic activity
Enzyme Commision number 3.5.1.-
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006338 chromatin remodeling

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vcg, PDBe:2vcg, PDBj:2vcg
PDBsum2vcg
PubMed18054239
UniProtQ70I53|HDAH_ALCSD Histone deacetylase-like amidohydrolase (Gene Name=hdaH)

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