Structure of PDB 4gfh Chain A Binding Site BS07

Receptor Information
>4gfh Chain A (length=1102) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTI
VPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPI
EIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEF
ILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRF
GMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLK
SLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQ
IVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTR
VKDFGSRCEIPLEYINKIMKTDLATRMFEIADANESRITNYPKLEDANKA
GTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREAS
ADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIK
GLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYE
KWREEESHKFTWKQKYYTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYID
LAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNI
RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQ
SLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNK
LTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWST
YIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGR
IEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDD
NIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNS
VNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELT
VTNKPRNAIIQELENLGFPRFNKEGKPYYGSEELYGTYEYLLGMRIWSLT
KERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAE
AR
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 chain4gfh Chain A Residue 1202 [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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PDB4gfh Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
Resolution4.408 Å
Binding residue
(original residue number in PDB)		N70 N74 I104 F121 S127 S128 G140 R141 N142 G143 Y144 G145 A146 K147 T195 Q365 K367
Binding residue
(residue number reindexed from 1)		N64 N68 I98 F115 S121 S122 G134 R135 N136 G137 Y138 G139 A140 K141 T189 Q342 K344
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:0006259 DNA metabolic process
GO:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4gfh, PDBe:4gfh, PDBj:4gfh
PDBsum4gfh
PubMed23022727
UniProtP06786|TOP2_YEAST DNA topoisomerase 2 (Gene Name=TOP2)

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