Structure of PDB 4gee Chain A Binding Site BS01

Receptor Information
>4gee 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 ID0WT
InChIInChI=1S/C17H18ClN7O/c1-2-11-13(18)12-15(22-11)23-17(26-8-3-20-7-21-4-8)24-16(12)25-5-9-10(6-25)14(9)19/h3-4,7,9-10,14H,2,5-6,19H2,1H3,(H,22,23,24)/t9-,10+,14+
InChIKeyYZRGALHCPBRTES-MSRIBSCDSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCc1[nH]c2nc(Oc3cncnc3)nc(N4C[CH]5[CH](N)[CH]5C4)c2c1Cl
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3C[C@@H]4[C@H](C3)C4N)Oc5cncnc5)Cl
ACDLabs 12.01Clc3c2c(nc(Oc1cncnc1)nc2nc3CC)N5CC4C(N)C4C5
CACTVS 3.370CCc1[nH]c2nc(Oc3cncnc3)nc(N4C[C@H]5[C@H](N)[C@H]5C4)c2c1Cl
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CC4C(C3)C4N)Oc5cncnc5)Cl
FormulaC17 H18 Cl N7 O
Name(1R,5S,6s)-3-[5-chloro-6-ethyl-2-(pyrimidin-5-yloxy)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-amine
ChEMBLCHEMBL2338001
DrugBank
ZINCZINC000103096070
PDB chain4gee Chain A Residue 301 [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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PDB4gee 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.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		N48 S49 E52 D75 R78 G79 I80 P81 T167 V169
Binding residue
(residue number reindexed from 1)		N31 S32 E35 D58 R61 G62 I63 P64 T133 V135
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:4gee, PDBe:4gee, PDBj:4gee
PDBsum4gee
PubMed23352267
UniProtQ839Z1|GYRB_ENTFA DNA gyrase subunit B (Gene Name=gyrB)

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