Structure of PDB 1ake Chain B Binding Site BS01

Receptor Information
>1ake Chain B (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
EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTK
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 chain1ake Chain B Residue 215 [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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PDB1ake Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		P9 G10 A11 G12 K13 T15 T31 L35 R36 M53 K57 L58 V59 V64 R88 Q92 R123 V132 Y133 H134 F137 R156 R167 V202
Binding residue
(residue number reindexed from 1)		P9 G10 A11 G12 K13 T15 T31 L35 R36 M53 K57 L58 V59 V64 R88 Q92 R123 V132 Y133 H134 F137 R156 R167 V202
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K13 R88 R123 R156 R167
Catalytic site (residue number reindexed from 1) K13 R88 R123 R156 R167
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004017 adenylate kinase activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016208 AMP binding
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0019205 nucleobase-containing compound kinase activity
GO:0050145 nucleoside monophosphate kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006172 ADP biosynthetic process
GO:0009123 nucleoside monophosphate metabolic process
GO:0009132 nucleoside diphosphate metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0015951 purine ribonucleotide interconversion
GO:0016310 phosphorylation
GO:0044209 AMP salvage
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ake, PDBe:1ake, PDBj:1ake
PDBsum1ake
PubMed1548697
UniProtP69441|KAD_ECOLI Adenylate kinase (Gene Name=adk)

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