Structure of PDB 4hxw Chain A Binding Site BS01

Receptor Information
>4hxw Chain A (length=191) Species: 226185 (Enterococcus faecalis V583) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEP
DDSITVIDDGRGIPVGIQAKTGRPAVETVFTVLVGSSVVNALSTSLDVRV
YKDGKVYYQEYRRGAVVDDLKVIEETDRHGTTVHFIPDPEIFTETTVYDF
DKLATRVRELAFLNRGLHISIEDRREGQEDKKEYHYEGLEH
Ligand information
Ligand ID1A0
InChIInChI=1S/C19H19ClN8S/c1-2-12-15(20)14-17(25-12)26-19(27-18(14)28-6-3-10(21)9-28)29-11-7-13-16(24-8-11)23-5-4-22-13/h4-5,7-8,10H,2-3,6,9,21H2,1H3,(H,25,26,27)/t10-/m1/s1
InChIKeyWXCUMDKJRMUULE-SNVBAGLBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCc1[nH]c2nc(Sc3cnc4nccnc4c3)nc(N5CC[C@@H](N)C5)c2c1Cl
CACTVS 3.370CCc1[nH]c2nc(Sc3cnc4nccnc4c3)nc(N5CC[CH](N)C5)c2c1Cl
ACDLabs 12.01Clc2c1c(nc(nc1nc2CC)Sc3cc4nccnc4nc3)N5CCC(N)C5
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nccn5)nc4)Cl
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CCC(C3)N)Sc4cc5c(nccn5)nc4)Cl
FormulaC19 H19 Cl N8 S
Name(3R)-1-[5-chloro-6-ethyl-2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]pyrrolidin-3-amine
ChEMBLCHEMBL2331855
DrugBank
ZINCZINC000095591180
PDB chain4hxw Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4hxw Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		N55 S56 E59 D82 R85 G86 I87 P88 T174
Binding residue
(residue number reindexed from 1)		N31 S32 E35 D58 R61 G62 I63 P64 T131
Annotation score1
Binding affinityMOAD: Ki=2nM
PDBbind-CN: -logKd/Ki=8.70,Ki=2nM
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:4hxw, PDBe:4hxw, PDBj:4hxw
PDBsum4hxw
PubMed23352267
UniProtQ839Z1|GYRB_ENTFA DNA gyrase subunit B (Gene Name=gyrB)

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