Structure of PDB 6zy7 Chain A Binding Site BS05

Receptor Information
>6zy7 Chain A (length=1159) 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
QSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKDK
LDETGNSLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDY
VADQIVTKLVDVVKKKNVKAHQVKNHMWIFVNALIENPTFDSQTKENMTL
QPKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFKAQVQLNKKCSAVKHN
RIKGIPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGV
FPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRY
GKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLRHRFLEEFITPIVKVSKN
KQEMAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSKEAKEYFADMKR
HRIQFKYSGPEDDAAISLAFSKKQIDDRKEWLTNFMEDRRQRKLLGLPED
YLYGQTTTYLTYNDFINKELILFSNSDNERSIPSMVDGLKPGQRKVLFTC
FKRNDKREVKVAQLAGSVAEMSSYHHGEMSLMMTIINLAQNFVGSNNLNL
LQPIGQFGTRLHGGKDSASPRYIFTMLSSLARLLFPPKDDHTLKFLYDDN
QRVEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGE
EPLPMLPSYKNFKGTIEELAPNQYVISGEVAILNSTTIEISELPVRTWTQ
TYKEQVLEPMLNGTEKTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERV
GLHKVFKLQTSLTCNSMVLFDHVGCLKKYDTVLDILRDFFELRLKYYGLR
KEWLLGMLGAESAKLNNQARFILEKIDGKIIIENKPKKELIKVLIQRGYD
SDPVKAWKEAQQKVSGPTFNYLLDMPLWYLTKEKKDELCRLRNEKEQELD
TLKRKSPSDLWKEDLATFIEELEAVEAKEKQDEQVGLPGKGGKAKGKKTQ
MAEVLPSPR
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 chain6zy7 Chain A Residue 1601 [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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PDB6zy7 Structural basis for allosteric regulation of Human Topoisomerase II alpha.
Resolution4.64 Å
Binding residue
(original residue number in PDB)		N91 N95 I125 I141 S148 S149 N150 G161 G164 Y165 G166 K168 T215 Q376 K378
Binding residue
(residue number reindexed from 1)		N63 N67 I97 I113 S120 S121 N122 G133 G136 Y137 G138 K140 T187 Q343 K345
Annotation score4
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005080 protein kinase C binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0008301 DNA binding, bending
GO:0042803 protein homodimerization activity
GO:0043130 ubiquitin binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity
Biological Process
GO:0000712 resolution of meiotic recombination intermediates
GO:0000819 sister chromatid segregation
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006259 DNA metabolic process
GO:0006265 DNA topological change
GO:0006266 DNA ligation
GO:0006974 DNA damage response
GO:0007059 chromosome segregation
GO:0007143 female meiotic nuclear division
GO:0030261 chromosome condensation
GO:0030263 apoptotic chromosome condensation
GO:0040016 embryonic cleavage
GO:0042752 regulation of circadian rhythm
GO:0043065 positive regulation of apoptotic process
GO:0045870 positive regulation of single stranded viral RNA replication via double stranded DNA intermediate
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048511 rhythmic process
GO:0060255 regulation of macromolecule metabolic process
GO:1905463 negative regulation of DNA duplex unwinding
Cellular Component
GO:0000228 nuclear chromosome
GO:0000775 chromosome, centromeric region
GO:0000793 condensed chromosome
GO:0001673 male germ cell nucleus
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005814 centriole
GO:0009330 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
GO:0032991 protein-containing complex
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6zy7, PDBe:6zy7, PDBj:6zy7
PDBsum6zy7
PubMed34016969
UniProtP11388|TOP2A_HUMAN DNA topoisomerase 2-alpha (Gene Name=TOP2A)

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