Structure of PDB 8q2b Chain A Binding Site BS01

Receptor Information
>8q2b Chain A (length=214) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAK
DIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAG
INVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
EELTTRKADQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTK
PVAEVRADLEKILG
Ligand information
Ligand IDAP5
InChIInChI=1S/C20H29N10O22P5/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(47-19)1-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-2-8-12(32)14(34)20(48-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyOIMACDRJUANHTJ-XPWFQUROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
FormulaC20 H29 N10 O22 P5
NameBIS(ADENOSINE)-5'-PENTAPHOSPHATE
ChEMBLCHEMBL437508
DrugBankDB01717
ZINCZINC000096085195
PDB chain8q2b Chain A Residue 301 [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]
PDB8q2b Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		P9 G10 G12 K13 G14 T15 T31 G32 L35 R36 M53 K57 L58 V59 V64 R88 Q92 R119 R123 V132 Y133 H134 F137 V202
Binding residue
(residue number reindexed from 1)		P9 G10 G12 K13 G14 T15 T31 G32 L35 R36 M53 K57 L58 V59 V64 R88 Q92 R119 R123 V132 Y133 H134 F137 V202
Annotation score4
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0050145 nucleoside monophosphate kinase activity
Biological Process
GO:0009123 nucleoside monophosphate metabolic process
GO:0009132 nucleoside diphosphate metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0044209 AMP salvage
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8q2b, PDBe:8q2b, PDBj:8q2b
PDBsum8q2b
PubMed38117131
UniProtP69441|KAD_ECOLI Adenylate kinase (Gene Name=adk)

[Back to BioLiP]