Structure of PDB 5g1a Chain B Binding Site BS02

Receptor Information
>5g1a Chain B (length=371) Species: 507 (Alcaligenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHAIGYVWNTLYGWVDTGTGSLAAANLTARMQPISHHLAHPDTKRRFHE
LVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGGDTGD
GITMMGNGGLEIARLSAGGAVELTRRVATGELSAGYALVNPPGHHAPHNA
AMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSVL
TISLHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHAMDQV
VLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAAD
ICDGRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAGMGGN
TLLDAERAAIEEIVPLLADIR
Ligand information
Ligand ID7H1
InChIInChI=1S/C14H8F12N2O3/c15-9(16,7(29)27-6-4-2-1-3-5-6)11(19,20)13(23,24)14(25,26)12(21,22)10(17,18)8(30)28-31/h1-5,31H,(H,27,29)(H,28,30)
InChIKeyPVEUUUJZCFCCIZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385ONC(=O)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)Nc1ccccc1
OpenEye OEToolkits 2.0.5c1ccc(cc1)NC(=O)C(C(C(C(C(C(C(=O)NO)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F
FormulaC14 H8 F12 N2 O3
Name2,2,3,3,4,4,5,5,6,6,7,7-dodecakis(fluoranyl)-~{N}-oxidanyl-~{N}'-phenyl-octanediamide
ChEMBLCHEMBL1934890
DrugBank
ZINCZINC000040163586
PDB chain5g1a Chain B Residue 373 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5g1a 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.
Resolution1.42 Å
Binding residue
(original residue number in PDB)		L21 I100 H142 H143 G151 F152 D180 H182 F208 Y312
Binding residue
(residue number reindexed from 1)		L23 I102 H144 H145 G153 F154 D182 H184 F210 Y314
Annotation score1
Binding affinityMOAD: Kd=0.27uM
PDBbind-CN: -logKd/Ki=6.57,Kd=0.27uM
BindingDB: Kd=540nM
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:5g1a, PDBe:5g1a, PDBj:5g1a
PDBsum5g1a
PubMed28389333
UniProtQ70I53|HDAH_ALCSD Histone deacetylase-like amidohydrolase (Gene Name=hdaH)

[Back to BioLiP]