Structure of PDB 4b6c Chain A Binding Site BS01

Receptor Information
>4b6c Chain A (length=161) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIP
VPTIDVVMTQVGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGG
ETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDER
DGKHRVFHYPG
Ligand information
Ligand IDB5U
InChIInChI=1S/C27H34N6O2/c1-19-5-6-21(17-20(19)2)24-18-29-27(25(31-24)26(28)34)30-22-7-9-23(10-8-22)35-16-4-11-33-14-12-32(3)13-15-33/h5-10,17-18H,4,11-16H2,1-3H3,(H2,28,34)(H,29,30)
InChIKeySMJHCUSNBTWDKM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1ccc(cc1C)c2cnc(c(n2)C(=O)N)Nc3ccc(cc3)OCCCN4CCN(CC4)C
CACTVS 3.385CN1CCN(CCCOc2ccc(Nc3ncc(nc3C(N)=O)c4ccc(C)c(C)c4)cc2)CC1
ACDLabs 12.01O=C(N)c2nc(c1ccc(c(c1)C)C)cnc2Nc4ccc(OCCCN3CCN(CC3)C)cc4
FormulaC27 H34 N6 O2
Name6-(3,4-dimethylphenyl)-3-[[4-[3-(4-methylpiperazin-1-yl)propoxy]phenyl]amino]pyrazine-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000095921141
PDB chain4b6c Chain A Residue 1256 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4b6c Aminopyrazinamides: novel and specific GyrB inhibitors that kill replicating and nonreplicating Mycobacterium tuberculosis.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N52 E56 R82 G83 I84 P85 Q102 V123 S126 T169
Binding residue
(residue number reindexed from 1)		N17 E21 R47 G48 I49 P50 Q60 V61 S64 T107
Annotation score1
Binding affinityMOAD: ic50=0.69uM
PDBbind-CN: -logKd/Ki=6.16,IC50=0.69uM
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4b6c, PDBe:4b6c, PDBj:4b6c
PDBsum4b6c
PubMed23268609
UniProtP0C559|GYRB_MYCSM DNA gyrase subunit B (Gene Name=gyrB)

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