Structure of PDB 3zkd Chain G Binding Site BS01

Receptor Information
>3zkd Chain G (length=378) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMA
GYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKF
DSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLK
QGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLT
DERVPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVE
IAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLL
PNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQL
THWFEANPTDAKVVVNKAVSSAQARIAA
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain3zkd Chain G Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zkd Mycobacterium Tuberculosis DNA Gyrase ATPase Domain Structures Suggest a Dissociative Mechanism that Explains How ATP Hydrolysis is Coupled to Domain Motion.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		N52 E56 G83 I84 V99 G106 G107 K108 Y114 G119 L120 H121 G122 V123 G124 V125 K372
Binding residue
(residue number reindexed from 1)		N43 E47 G74 I75 V90 G97 G98 K99 Y105 G110 L111 H112 G113 V114 G115 V116 K330
Annotation score4
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3zkd, PDBe:3zkd, PDBj:3zkd
PDBsum3zkd
PubMed24015710
UniProtP9WG45|GYRB_MYCTU DNA gyrase subunit B (Gene Name=gyrB)

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