Structure of PDB 4hym Chain A Binding Site BS01

Receptor Information
>4hym Chain A (length=361) Species: 376619 (Francisella tularensis subsp. holarctica LVS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINI
TLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSNGGLHG
VGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGT
KIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTW
HFETGLKGYLDHKLEAETLPAEPFIIDNFSNGDSYLDAVFCWCEDPSESI
KNSYVNLIPTPQDGTHVTGLKNGIYDAIKAYIEKNSNIKITANDSFAQLN
YVISVKITNPQFAGQTKEKLSNKDVTNFVATAVKDLLTIWLNQNPDEARQ
IVENISKVAQK
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 chain4hym Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4hym 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 G72 M73 I89 T162 I164
Binding residue
(residue number reindexed from 1)		I32 N35 S36 E39 D62 G66 M67 I83 T150 I152
Annotation score1
Binding affinityMOAD: Ki=6nM
PDBbind-CN: -logKd/Ki=8.22,Ki=6nM
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:4hym, PDBe:4hym, PDBj:4hym
PDBsum4hym
PubMed23352267
UniProtA0A0J9WZF0|PARE_FRATH DNA topoisomerase 4 subunit B (Gene Name=parE)

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