Structure of PDB 5gwj Chain A Binding Site BS05

Receptor Information
>5gwj Chain A (length=677) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPITSTAKEAK
EYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQR
RLHGLKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFK
RNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQ
PIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQR
VEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDP
HPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVY
KEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGL
HKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKE
WLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESD
PVKAWKEAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRK
SPSDLWKEDLAAFVEELDKVESQERED
Ligand information
Ligand IDN2W
InChIInChI=1S/C26H31N3O8.ClH.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);1H;/q;;+1/p-1/t13-,16+,22-,23-,24-;;/m1../s1
InChIKeyUVMRTXMJNLJFNR-JLXFAVSYSA-M
SMILES
SoftwareSMILES
ACDLabs 12.01COc1c(c(cc(c1)C2C6C(C(c4c2cc3c(OCO3)c4)NC(=O)CCC5CN[Pt](Cl)N5)COC6=O)OC)O
OpenEye OEToolkits 1.7.6COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)NC(=O)CCC6C[NH2][Pt]([NH2]6)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)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)c5cc6OCOc6cc25
CACTVS 3.385COc1cc(cc(OC)c1O)[CH]2[CH]3[CH](COC3=O)[CH](NC(=O)CC[CH]4N|[Pt](|NC4)Cl)c5cc6OCOc6cc25
FormulaC26 H31 Cl N3 O8 Pt
Namechloro{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 chain5gwj Chain A Residue 1302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5gwj Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry
Resolution2.566 Å
Binding residue
(original residue number in PDB)
G478 D479 R503 Q778 M782
Binding residue
(residue number reindexed from 1)
G27 D28 R52 Q277 M281
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:5gwj, PDBe:5gwj, PDBj:5gwj
PDBsum5gwj
PubMed28977631
UniProtQ02880|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)

[Back to BioLiP]