Structure of PDB 4bae Chain B Binding Site BS01

Receptor Information
>4bae Chain B (length=183) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHA
DGSVEVRDDGRGIPVEMHATGMPTIDVVMTQLGVGVSVVNALSTRLEATV
LRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFET
VARRLQEMAFLNKGLTIELTDERDGKHRVFHYP
Ligand information
Ligand IDRWX
InChIInChI=1S/C19H21BrClN7O4S/c1-8-12(21)11(20)13(24-8)17(29)25-9-4-5-28(6-10(9)32-3)19-26-14(15(33-19)18(30)31)16-22-7-23-27(16)2/h7,9-10,24H,4-6H2,1-3H3,(H,25,29)(H,30,31)/t9-,10+/m1/s1
InChIKeyIXOKPDRRYHAGRW-ZJUUUORDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Brc1c(Cl)c(nc1C(=O)NC4C(OC)CN(c2nc(c(s2)C(=O)O)c3ncnn3C)CC4)C
OpenEye OEToolkits 1.9.2Cc1c(c(c([nH]1)C(=O)NC2CCN(CC2OC)c3nc(c(s3)C(=O)O)c4ncnn4C)Br)Cl
OpenEye OEToolkits 1.9.2Cc1c(c(c([nH]1)C(=O)N[C@@H]2CCN(C[C@@H]2OC)c3nc(c(s3)C(=O)O)c4ncnn4C)Br)Cl
CACTVS 3.385CO[CH]1CN(CC[CH]1NC(=O)c2[nH]c(C)c(Cl)c2Br)c3sc(C(O)=O)c(n3)c4ncnn4C
CACTVS 3.385CO[C@H]1CN(CC[C@H]1NC(=O)c2[nH]c(C)c(Cl)c2Br)c3sc(C(O)=O)c(n3)c4ncnn4C
FormulaC19 H21 Br Cl N7 O4 S
Name2-[(3S,4R)-4-[(3-bromanyl-4-chloranyl-5-methyl-1H-pyrrol-2-yl)carbonylamino]-3-methoxy-piperidin-1-yl]-4-(2-methyl-1,2,4-triazol-3-yl)-1,3-thiazole-5-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000068207424
PDB chain4bae Chain B Residue 1255 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4bae Optimization of Pyrrolamides as Mycobacterial Gyrb ATPase Inhibitors: Structure Activity Relationship and in Vivo Efficacy in the Mouse Model of Tuberculosis.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		V49 N52 E56 D79 R82 G83 I84 P85 V125 R141 T169
Binding residue
(residue number reindexed from 1)		V28 N31 E35 D58 R61 G62 I63 P64 V86 R102 T130
Annotation score1
Binding affinityMOAD: ic50=3nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4bae, PDBe:4bae, PDBj:4bae
PDBsum4bae
PubMed24126580
UniProtP0C559|GYRB_MYCSM DNA gyrase subunit B (Gene Name=gyrB)

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