Structure of PDB 3zkd Chain A Binding Site BS01

Receptor Information
>3zkd Chain A (length=377) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGY
ATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDS
DAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQG
APTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDE
RHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQ
WNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKDPNLTG
DDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFE
ANPTDAKVVVNKAVSSAQARIAARKAR
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 A 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 I84 V99 G106 G107 K108 Y114 G119 L120 H121 G122 V123 G124 V125 S169 K372
Binding residue
(residue number reindexed from 1)		N41 E45 I73 V88 G95 G96 K97 Y103 G108 L109 H110 G111 V112 G113 V114 S158 K325
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
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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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