Structure of PDB 4efb Chain A Binding Site BS02

Receptor Information
>4efb Chain A (length=313) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIET
EFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDER
VRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENL
RTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNA
AAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRT
NPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFT
VKAPRWAIAYKFP
Ligand information
Ligand ID0OW
InChIInChI=1S/C15H22N4O4/c16-12-11(13(17)21)14(23-10-7-3-6-9(10)20)19-15(18-12)22-8-4-1-2-5-8/h8-10,20H,1-7H2,(H2,17,21)(H2,16,18,19)/t9-,10+/m0/s1
InChIKeyGOYBCUMANOWCAY-VHSXEESVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1CCC(C1)Oc2nc(c(c(n2)O[C@@H]3CCC[C@@H]3O)C(=O)N)N
ACDLabs 12.01O=C(c3c(OC1CCCC1O)nc(OC2CCCC2)nc3N)N
CACTVS 3.370NC(=O)c1c(N)nc(OC2CCCC2)nc1O[C@@H]3CCC[C@@H]3O
OpenEye OEToolkits 1.7.6C1CCC(C1)Oc2nc(c(c(n2)OC3CCCC3O)C(=O)N)N
CACTVS 3.370NC(=O)c1c(N)nc(OC2CCCC2)nc1O[CH]3CCC[CH]3O
FormulaC15 H22 N4 O4
Name4-amino-2-(cyclopentyloxy)-6-{[(1R,2S)-2-hydroxycyclopentyl]oxy}pyrimidine-5-carboxamide
ChEMBL
DrugBank
ZINCZINC000095920817
PDB chain4efb Chain A Residue 404 [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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PDB4efb Crystal structure of DNA ligase
Resolution2.2 Å
Binding residue
(original residue number in PDB)		L89 K120 I121 R141 Y227 V289 K291
Binding residue
(residue number reindexed from 1)		L85 K116 I117 R137 Y223 V285 K287
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E118 K120 D122 Y227 K315
Catalytic site (residue number reindexed from 1) E114 K116 D118 Y223 K311
Enzyme Commision number 6.5.1.2: DNA ligase (NAD(+)).
Gene Ontology
Molecular Function
GO:0003911 DNA ligase (NAD+) activity

View graph for
Molecular Function
External links
PDB RCSB:4efb, PDBe:4efb, PDBj:4efb
PDBsum4efb
PubMed
UniProtQ837V6|DNLJ_ENTFA DNA ligase (Gene Name=ligA)

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