Structure of PDB 2vcg Chain A Binding Site BS03

Receptor Information
>2vcg Chain A (length=368) Species: 512 (Alcaligenes sp.) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HAIGYVWNTLYGWVDTGTGSLAAANLTARMQPISHHLAHPDTKRRFHELV
CASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGGDTGDGI
TMMGNGGLEIARLSAGGAVELTRRVATGELSAGYALVNPPGHHAPHNAAM
GFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSVLTI
SLHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHAMDQVVL
PALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAADIC
DGRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAGMGGNTL
LDAERAAIEEIVPLLADI
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)		Y344 E346 F347
Binding residue
(residue number reindexed from 1)		Y338 E340 F341
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

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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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