Structure of PDB 3fci Chain A Binding Site BS01

Receptor Information
>3fci Chain A (length=223) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQM
CDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDI
EDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVS
WLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGC
RHFSKTNELLQKSGKKPIDWKEL
Ligand information
Ligand ID3FI
InChIInChI=1S/C16H18N4O5/c21-14-8-13(19-16(24)20-14)10-17-5-2-6-25-18-9-11-3-1-4-12(7-11)15(22)23/h1,3-4,7-9,17H,2,5-6,10H2,(H,22,23)(H2,19,20,21,24)/b18-9+
InChIKeyDNNMFLCWPRQYIC-GIJQJNRQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=O)O)\C=N\OCCCNCC2=CC(=O)NC(=O)N2
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=O)O)C=NOCCCNCC2=CC(=O)NC(=O)N2
CACTVS 3.341OC(=O)c1cccc(C=NOCCCNCC2=CC(=O)NC(=O)N2)c1
CACTVS 3.341OC(=O)c1cccc(\C=N\OCCCNCC2=CC(=O)NC(=O)N2)c1
ACDLabs 10.04O=C1NC(=CC(=O)N1)CNCCCO\N=C\c2cccc(C(=O)O)c2
FormulaC16 H18 N4 O5
Name3-{(E)-[(3-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}propoxy)imino]methyl}benzoic acid
ChEMBLCHEMBL1213370
DrugBank
ZINCZINC000058592582
PDB chain3fci Chain A Residue 1 [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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PDB3fci Impact of linker strain and flexibility in the design of a fragment-based inhibitor
Resolution1.27 Å
Binding residue
(original residue number in PDB)		G143 D145 Y147 C157 F158 N204 G246 S247 H268 S273
Binding residue
(residue number reindexed from 1)		G62 D64 Y66 C76 F77 N123 G165 S166 H187 S192
Annotation score1
Binding affinityMOAD: ic50=1.3uM
PDBbind-CN: -logKd/Ki=5.89,IC50=1.3uM
BindingDB: IC50=1.3e+3nM
Enzymatic activity
Catalytic site (original residue number in PDB) D145 Y147 F158 H268
Catalytic site (residue number reindexed from 1) D64 Y66 F77 H187
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:3fci, PDBe:3fci, PDBj:3fci
PDBsum3fci
PubMed19396178
UniProtP13051|UNG_HUMAN Uracil-DNA glycosylase (Gene Name=UNG)

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