Structure of PDB 6fu1 Chain A Binding Site BS02

Receptor Information
>6fu1 Chain A (length=395) Species: 6183 (Schistosoma mansoni) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVGIVYGDQYRQLCCSSPKFGDRYALVMDLINAYKLIPELSRVPPLQWDS
PSRMYEAVTAFHSTEYVDALKKLQMLHCEEKELTADDELLMDSFSLNYDC
PGFPSVFDYSLAAVQGSLAAASALICRHCEVVINWGGGWHHAKRSEASGF
CYLNDIVLAIHRLVSSQTRVLYVDLDLHHGDGVEEAFWYSPRVVTFSVHH
ASPGFFPGTGTWNFLNGAGRGRFSAFNLPLEEGINDLDWSNAIGPILDSL
NIVIQPSYVVVQCGADCLATDPHRIFRLTNFYPLSGYLYAIKKILSWKVP
TLILGGGGYNFPDTARLWTRVTALTIEEVKGKKMTISPEIPEHSYFSRYG
PDFELDIDYFPDSIQKHHRRILEQLRNYADLNKLIYDYDQVYQLY
Ligand information
Ligand IDE7Q
InChIInChI=1S/C16H19ClN2O4/c1-2-3-4-5-14(20)19(23)13-10-15(21)18(16(13)22)12-8-6-11(17)7-9-12/h6-9,13,23H,2-5,10H2,1H3/t13-/m0/s1
InChIKeyZAMVBYSBDZJLIX-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCC(=O)N([C@H]1CC(=O)N(C1=O)c2ccc(cc2)Cl)O
CACTVS 3.385CCCCCC(=O)N(O)[CH]1CC(=O)N(C1=O)c2ccc(Cl)cc2
OpenEye OEToolkits 2.0.6CCCCCC(=O)N(C1CC(=O)N(C1=O)c2ccc(cc2)Cl)O
CACTVS 3.385CCCCCC(=O)N(O)[C@H]1CC(=O)N(C1=O)c2ccc(Cl)cc2
FormulaC16 H19 Cl N2 O4
Name~{N}-[(3~{S})-1-(4-chlorophenyl)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-~{N}-oxidanyl-hexanamide
ChEMBLCHEMBL4963274
DrugBank
ZINCZINC000005190032
PDB chain6fu1 Chain A Residue 504 [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]
PDB6fu1 A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified by Structure-Based Virtual Screening and In Vitro Testing.
Resolution1.548 Å
Binding residue
(original residue number in PDB)		D100 G139 W140 H141 H142 G150 F151 D186 H188 F216 H292 G338 G339 Y341
Binding residue
(residue number reindexed from 1)		D99 G138 W139 H140 H141 G149 F150 D176 H178 F206 H273 G306 G307 Y309
Annotation score1
Binding affinityMOAD: ic50=4.4uM
PDBbind-CN: -logKd/Ki=5.36,IC50=4.4uM
Enzymatic activity
Enzyme Commision number 3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0046872 metal ion binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006338 chromatin remodeling
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fu1, PDBe:6fu1, PDBj:6fu1
PDBsum6fu1
PubMed29498707
UniProtA5H660

[Back to BioLiP]