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BioLiP

Structure of PDB 8yon Chain D Binding Site BS03

Receptor Information
>8yon Chain D (length=605) Species: 10666 (Enterobacteria phage T6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKNEIKILSDIEHIKKRSGMYIGSSANEMHERFLFGKWESVQYVPGLVK
LIDEIIDNSVDEGIRTKFKFANKINVTIKNNQVTVEDNGRGIPQAMVKTP
TGEEIPGPVAAWTIPKAGGNFGDDKERVTGGMNGVGSSLTNIFSVMFVGE
TGDGQNNIVVRCSNGMENKSWETIPGKWKGTRVTFIPDFMSFETNELSQV
YLDITLDRLQTLAVVYPDIQFTFNGKKVQGNFKKYARQYDEHAIVQEQEN
CSIAVGRSPDGFRQLTYVNNIHTKNGGHHIDCVMDDICEDLIPQIKRKFK
IDVTKARVKECLTIVMFVRDMKNMRFDSQTKERLTSPFGEIRSHIQLDAK
KISRAILNNEAILMPIIEAALARKLAAEKAAETKAAKKASKAKVHKHIKA
NLCGKDADTTLFLTEGDSAIGYLIDVRDKELHGGYPLRGKVLNSWGMSYA
DMLKNKELFDICAITGLVLGEKAENLNYHNIAIMTDADHDGLGSIYPSLL
GFFSNWPELFEQGRIRFVKTPVIIAHVGKKQEWFYTVAEYESAKDALPKH
SIRYIKGLGSLEKSEYREMIQNPVYDVVKLPENWKELFEMLMGDNADLRK
EWMSQ
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 chain8yon Chain D Residue 701 [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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PDB8yon structure of phage T6 full-length topoisomerase II bound with DNA
Resolution6.73 Å
Binding residue
(original residue number in PDB)		E54 N58 R65 W112 N120 G131 M132 N133 G134 G136 S137 Q329 K331
Binding residue
(residue number reindexed from 1)		E54 N58 R65 W112 N120 G131 M132 N133 G134 G136 S137 Q329 K331
Annotation score4
External links

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