Structure of PDB 5g17 Chain A Binding Site BS02

Receptor Information
>5g17 Chain A (length=368) Species: 507 (Alcaligenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIGYVWNTLYGWVDTGTGSLAAANLTARMQPISHHLAHPDTKRRFHELVC
ASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGGDTGDGIA
MMGNGGLEIARLSAGGAVELTRRVATGELSAGYALVNPPGHHAPHNAAMG
FCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSVLTIS
LHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHAMDQVVLP
ALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAADICD
GRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAGMGGNTLL
DAERAAIEEIVPLLADIR
Ligand information
Ligand ID6DK
InChIInChI=1S/C15H20F3NO3/c16-15(17,18)14(21,22)11-7-2-1-6-10-13(20)19-12-8-4-3-5-9-12/h3-5,8-9,21-22H,1-2,6-7,10-11H2,(H,19,20)
InChIKeyDOVGAPNVSPZBAT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1ccc(cc1)NC(=O)CCCCCCC(C(F)(F)F)(O)O
CACTVS 3.385OC(O)(CCCCCCC(=O)Nc1ccccc1)C(F)(F)F
FormulaC15 H20 F3 N O3
Name9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide
ChEMBL
DrugBank
ZINCZINC000584904690
PDB chain5g17 Chain A Residue 373 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5g17 The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket.
Resolution1.51 Å
Binding residue
(original residue number in PDB)		P140 H142 H143 G151 F152 D180 H182 F208 G310 Y312
Binding residue
(residue number reindexed from 1)		P139 H141 H142 G150 F151 D179 H181 F207 G309 Y311
Annotation score1
Binding affinityMOAD: Kd=0.2uM
PDBbind-CN: -logKd/Ki=6.70,Kd=0.2uM
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
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Biological Process
External links
PDB RCSB:5g17, PDBe:5g17, PDBj:5g17
PDBsum5g17
PubMed28389333
UniProtQ70I53|HDAH_ALCSD Histone deacetylase-like amidohydrolase (Gene Name=hdaH)

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