Structure of PDB 4hy1 Chain B Binding Site BS01

Receptor Information
>4hy1 Chain B (length=228) Species: 376619 (Francisella tularensis subsp. holarctica LVS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINIT
LYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSVGVSVVN
ALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPN
KKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLK
GYLDHKLAETLPAEPSESIKNSYVNLIP
Ligand information
Ligand ID19X
InChIInChI=1S/C20H19ClN6OS/c1-2-14-16(21)15-17(24-14)25-20(26-18(15)27-6-5-11(22)9-27)29-12-4-3-10-8-23-19(28)13(10)7-12/h3-4,7-8,11H,2,5-6,9,22H2,1H3,(H,24,25,26)/t11-/m1/s1
InChIKeyMFHNBYVWNDLIQC-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CCC(C3)N)Sc4ccc5c(c4)C(=O)N=C5)Cl
OpenEye OEToolkits 1.7.6CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4ccc5c(c4)C(=O)N=C5)Cl
CACTVS 3.370CCc1[nH]c2nc(Sc3ccc4C=NC(=O)c4c3)nc(N5CC[CH](N)C5)c2c1Cl
ACDLabs 12.01O=C5N=Cc4c5cc(Sc1nc3c(c(n1)N2CCC(N)C2)c(Cl)c(n3)CC)cc4
CACTVS 3.370CCc1[nH]c2nc(Sc3ccc4C=NC(=O)c4c3)nc(N5CC[C@@H](N)C5)c2c1Cl
FormulaC20 H19 Cl N6 O S
Name6-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)-1H-isoindol-1-one
ChEMBL
DrugBank
ZINCZINC000095921199
PDB chain4hy1 Chain B Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4hy1 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.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I38 N41 S42 E45 D68 R71 G72 M73 R131 T162
Binding residue
(residue number reindexed from 1)		I31 N34 S35 E38 D61 R64 G65 M66 R112 T143
Annotation score1
Binding affinityMOAD: 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
Cellular Component
GO:0005694 chromosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4hy1, PDBe:4hy1, PDBj:4hy1
PDBsum4hy1
PubMed23352267
UniProtA0A0J9WZF0|PARE_FRATH DNA topoisomerase 4 subunit B (Gene Name=parE)

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