Structure of PDB 4r1f Chain D Binding Site BS01

Receptor Information
>4r1f Chain D (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFV
PGLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVV
EHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFT
VETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKM
QSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKKV
IHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDYVADQIVTKLV
DVVKKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEK
FIKAAIGCGIVWVKFKAQVQLNK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4r1f Chain D Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r1f Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis
Resolution2.51 Å
Binding residue
(original residue number in PDB)		N91 N95 I125 I141 F142 S148 S149 G161 G164 G166 A167 K168
Binding residue
(residue number reindexed from 1)		N63 N67 I97 I113 F114 S120 S121 G133 G136 G138 A139 K140
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4r1f, PDBe:4r1f, PDBj:4r1f
PDBsum4r1f
PubMed25202966
UniProtP11388|TOP2A_HUMAN DNA topoisomerase 2-alpha (Gene Name=TOP2A)

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