Structure of PDB 1mx0 Chain E Binding Site BS01

Receptor Information
>1mx0 Chain E (length=456) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGIL
PNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQ
TRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEP
IIVERGSVENTFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIF
KDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIK
EFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYED
FRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAG
VAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESD
QYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYL
SEKRKE
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 chain1mx0 Chain E Residue 940 [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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PDB1mx0 Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N42 A46 I81 A89 S96 S97 K98 G106 M107 Y108 G109 L110 G111 V112 K113 T170 K427
Binding residue
(residue number reindexed from 1)		N39 A43 I78 A86 S93 S94 K95 G103 M104 Y105 G106 L107 G108 V109 K110 T165 K422
Annotation score4
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
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
View graph for
Biological Process
External links
PDB RCSB:1mx0, PDBe:1mx0, PDBj:1mx0
PDBsum1mx0
PubMed12505993
UniProtO05207|TOP6B_SACSH Type 2 DNA topoisomerase 6 subunit B (Gene Name=top6B)

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