Structure of PDB 3bab Chain A Binding Site BS02

Receptor Information
>3bab Chain A (length=312) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETE
FPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERV
RKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLR
TVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAA
AGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTN
PERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTV
KAPRWAIAYKFP
Ligand information
Ligand ID3BD
InChIInChI=1S/C20H25N9O/c1-20(2,3)18-26-16-13(11-12(15(22)30)14(21)25-16)17(27-18)28-7-9-29(10-8-28)19-23-5-4-6-24-19/h4-6,11H,7-10H2,1-3H3,(H2,22,30)(H2,21,25,26,27)
InChIKeyCKLCIJCZOIDJQU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(N)c1cc4c(nc1N)nc(nc4N3CCN(c2ncccn2)CC3)C(C)(C)C
OpenEye OEToolkits 1.5.0CC(C)(C)c1nc2c(cc(c(n2)N)C(=O)N)c(n1)N3CCN(CC3)c4ncccn4
CACTVS 3.341CC(C)(C)c1nc2nc(N)c(cc2c(n1)N3CCN(CC3)c4ncccn4)C(N)=O
FormulaC20 H25 N9 O
Name7-amino-2-tert-butyl-4-(4-pyrimidin-2-ylpiperazin-1-yl)pyrido[2,3-d]pyrimidine-6-carboxamide
ChEMBL
DrugBankDB07043
ZINCZINC000053683800
PDB chain3bab Chain A Residue 501 [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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PDB3bab Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L89 K120 I121 A125 E175 Y227 K291 W310
Binding residue
(residue number reindexed from 1)		L84 K115 I116 A120 E170 Y222 K286 W305
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E118 K120 D122 Y227 K315
Catalytic site (residue number reindexed from 1) E113 K115 D117 Y222 K310
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:3bab, PDBe:3bab, PDBj:3bab
PDBsum3bab
PubMed
UniProtQ837V6|DNLJ_ENTFA DNA ligase (Gene Name=ligA)

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