Structure of PDB 4ggl Chain A Binding Site BS01

Receptor Information
>4ggl Chain A (length=193) Species: 226185 (Enterococcus faecalis V583) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEP
DDSITVIDDGRGIPVGIQAKTGRPAVETVFTVLHGVGSSVVNALSTSLDV
RVYKDGKVYYQEYRRGAVVDDLKVIEETDRHGTTVHFIPDPEIFTETTVY
DFDKLATRVRELAFLNRGLHISIEDRREGQEDKKEYHYEGLEH
Ligand information
Ligand IDCJC
InChIInChI=1S/C19H19ClN8OS/c1-2-11-15(20)14-17(25-11)26-19(27-18(14)28-4-3-9(21)8-28)30-10-5-12-16(22-6-10)23-7-13(29)24-12/h5-7,9H,2-4,8,21H2,1H3,(H,24,29)(H,25,26,27)/t9-/m1/s1
InChIKeyQARZTJJXVNQVNZ-SECBINFHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C4Nc5cc(Sc1nc3c(c(n1)N2CCC(N)C2)c(Cl)c(n3)CC)cnc5N=C4
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nc4)N=CC(=O)N5)Cl
CACTVS 3.370CCc1[nH]c2nc(Sc3cnc4N=CC(=O)Nc4c3)nc(N5CC[CH](N)C5)c2c1Cl
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CCC(C3)N)Sc4cc5c(nc4)N=CC(=O)N5)Cl
CACTVS 3.370CCc1[nH]c2nc(Sc3cnc4N=CC(=O)Nc4c3)nc(N5CC[C@@H](N)C5)c2c1Cl
FormulaC19 H19 Cl N8 O S
Name7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)pyrido[2,3-b]pyrazin-2(1H)-one
ChEMBLCHEMBL2331826
DrugBank
ZINCZINC000095588604
PDB chain4ggl 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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PDB4ggl 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)		N48 S49 E52 D75 R78 G79 I80 P81 T167
Binding residue
(residue number reindexed from 1)		N31 S32 E35 D58 R61 G62 I63 P64 T133
Annotation score1
Binding affinityMOAD: Ki<1nM
PDBbind-CN: -logKd/Ki=9.00,Ki<1nM
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:4ggl, PDBe:4ggl, PDBj:4ggl
PDBsum4ggl
PubMed23352267
UniProtQ839Z1|GYRB_ENTFA DNA gyrase subunit B (Gene Name=gyrB)

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