Structure of PDB 1pvg Chain B Binding Site BS01

Receptor Information
>1pvg Chain B (length=378) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIV
PGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIE
IHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFI
LETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFG
MKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKS
LEIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQ
IVKKISEILKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDF
GSRCEIPLEYINKIMKTDLATRMFEIAD
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 chain1pvg Chain B Residue 902 [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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PDB1pvg Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187
Resolution1.8 Å
Binding residue
(original residue number in PDB)		N70 N74 N99 I104 I120 F121 S127 S128 G140 R141 N142 G143 Y144 G145 A146 K147 Q365 K367
Binding residue
(residue number reindexed from 1)		N63 N67 N92 I97 I113 F114 S120 S121 G133 R134 N135 G136 Y137 G138 A139 K140 Q338 K340
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:1pvg, PDBe:1pvg, PDBj:1pvg
PDBsum1pvg
PubMed12963818
UniProtP06786|TOP2_YEAST DNA topoisomerase 2 (Gene Name=TOP2)

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