Structure of PDB 5gwi Chain A Binding Site BS03

Receptor Information
>5gwi Chain A (length=671) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITKEAKEYFADM
ERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLK
HLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKRE
VKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFG
TRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWY
IPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPN
YKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLE
PMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKL
QTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGML
GAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWK
EAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLW
KEDLAAFVEELDKVESQERED
Ligand information
Ligand IDN2R
InChIInChI=1S/C26H31N3O8.2ClH.Pt/c1-33-19-5-12(6-20(34-2)25(19)31)22-14-7-17-18(37-11-36-17)8-15(14)24(16-10-35-26(32)23(16)22)29-21(30)4-3-13(28)9-27;;;/h5-8,13,16,22-24,31H,3-4,9-11,27-28H2,1-2H3,(H,29,30);2*1H;/q;;;+2/p-2/t13-,16-,22+,23-,24-;;;/m0.../s1
InChIKeyPTKKCRGGEZZAPV-FTKFZVBUSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)NC(=O)CCC6C[NH2][Pt]([NH2]6)(Cl)Cl)OCO4
OpenEye OEToolkits 1.7.6COc1cc(cc(c1O)OC)[C@@H]2c3cc4c(cc3[C@@H]([C@@H]5[C@@H]2C(=O)OC5)NC(=O)CC[C@H]6C[NH2][Pt]([NH2]6)(Cl)Cl)OCO4
CACTVS 3.385COc1cc(cc(OC)c1O)[C@H]2[C@@H]3[C@H](COC3=O)[C@@H](NC(=O)CC[C@@H]4N|[Pt](|NC4)(Cl)Cl)c5cc6OCOc6cc25
CACTVS 3.385COc1cc(cc(OC)c1O)[CH]2[CH]3[CH](COC3=O)[CH](NC(=O)CC[CH]4N|[Pt](|NC4)(Cl)Cl)c5cc6OCOc6cc25
ACDLabs 12.01Cl[Pt]6(Cl)NCC(CCC(NC2c5c(C(c1cc(OC)c(c(c1)OC)O)C3C2COC3=O)cc4OCOc4c5)=O)N6
FormulaC26 H31 Cl2 N3 O8 Pt
Namedichloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl]pentanamide}platinum
ChEMBL
DrugBank
ZINC
PDB chain5gwi Chain A Residue 1301 [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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PDB5gwi Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry
Resolution2.737 Å
Binding residue
(original residue number in PDB)
G478 R503 Q778 M782
Binding residue
(residue number reindexed from 1)
G27 R52 Q271 M275
Annotation score1
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:0006259 DNA metabolic process
GO:0006265 DNA topological change

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5gwi, PDBe:5gwi, PDBj:5gwi
PDBsum5gwi
PubMed28977631
UniProtQ02880|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)

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