Structure of PDB 3fcl Chain B Binding Site BS02

Receptor Information
>3fcl Chain B (length=222) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMC
DIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIE
DFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSW
LNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCR
HFSKTNELLQKSGKKPIDWKEL
Ligand information
Ligand ID3FL
InChIInChI=1S/C17H22N4O4/c22-15-9-14(20-17(25)21-15)11-19-7-2-1-6-18-10-12-4-3-5-13(8-12)16(23)24/h3-5,8-9,18-19H,1-2,6-7,10-11H2,(H,23,24)(H2,20,21,22,25)
InChIKeyPLKKHOGCWCJFJX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=O)O)CNCCCCNCC2=CC(=O)NC(=O)N2
ACDLabs 10.04O=C1NC(=CC(=O)N1)CNCCCCNCc2cc(C(=O)O)ccc2
CACTVS 3.341OC(=O)c1cccc(CNCCCCNCC2=CC(=O)NC(=O)N2)c1
FormulaC17 H22 N4 O4
Name3-{[(4-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}butyl)amino]methyl}benzoic acid
ChEMBLCHEMBL1213373
DrugBank
ZINCZINC000058583506
PDB chain3fcl Chain B Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3fcl Impact of linker strain and flexibility in the design of a fragment-based inhibitor
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G143 Q144 D145 Y147 C157 F158 N204 H268 S270
Binding residue
(residue number reindexed from 1)		G61 Q62 D63 Y65 C75 F76 N122 H186 S188
Annotation score1
Binding affinityMOAD: ic50=315uM
BindingDB: IC50=3.15e+5nM
Enzymatic activity
Catalytic site (original residue number in PDB) D145 Y147 F158 H268
Catalytic site (residue number reindexed from 1) D63 Y65 F76 H186
Enzyme Commision number 3.2.2.27: uracil-DNA glycosylase.
Gene Ontology
Molecular Function
GO:0004844 uracil DNA N-glycosylase activity
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3fcl, PDBe:3fcl, PDBj:3fcl
PDBsum3fcl
PubMed19396178
UniProtP13051|UNG_HUMAN Uracil-DNA glycosylase (Gene Name=UNG)

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