Structure of PDB 4efe Chain A Binding Site BS02

Receptor Information

>4efe Chain A (length=313) Species: 1351 (Enterococcus faecalis)

PLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIET
EFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDER
VRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENL
RTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNA
AAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRT
NPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFT
VKAPRWAIAYKFP

Ligand information

• Ligand ID: 0OV
• InChI: InChI=1S/C16H19N5O2/c1-10-4-2-3-5-12(10)23-16-19-14(18)13-11(22)6-8-21(9-7-17)15(13)20-16/h6,8,10,12H,2-5,9H2,1H3,(H2,18,19,20)/t10-,12+/m1/s1
• InChIKey: MZUFVSMPTFUMGZ-PWSUYJOCSA-N
• SMILES:
  CACTVS 3.370: C[C@@H]1CCCC[C@@H]1Oc2nc(N)c3C(=O)C=CN(CC#N)c3n2
  OpenEye OEToolkits 1.7.6: C[C@@H]1CCCC[C@@H]1Oc2nc(c3c(n2)N(C=CC3=O)CC#N)N
  ACDLabs 12.01: O=C3c1c(nc(nc1N)OC2CCCCC2C)N(C=C3)CC#N
  OpenEye OEToolkits 1.7.6: CC1CCCCC1Oc2nc(c3c(n2)N(C=CC3=O)CC#N)N
  CACTVS 3.370: C[CH]1CCCC[CH]1Oc2nc(N)c3C(=O)C=CN(CC#N)c3n2
• Formula: C16 H19 N5 O2
• Name: [4-amino-2-{[(1S,2R)-2-methylcyclohexyl]oxy}-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl]acetonitrile
• ZINC: ZINC000095920548
• PDB chain: 4efe Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4efe crystal structure of DNA ligase
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): L89 K120 I121 E175 Y227 K291 P308 W310
• Binding residue (residue number reindexed from 1): L85 K116 I117 E171 Y223 K287 P304 W306
• Annotation score: 1

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

External links

• PDB: RCSB:4efe, PDBe:4efe, PDBj:4efe
• PDBsum: 4efe
• UniProt: Q837V6|DNLJ_ENTFA DNA ligase (Gene Name=ligA)