Structure of PDB 1z83 Chain B Binding Site BS03

Receptor Information
>1z83 Chain B (length=195) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMEEKLKKTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSS
GSARGKKLSEIMEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREV
QQGEEFERRIGQPTLLLYVDAGPETMTQRLLKRGETSGRVDDNEETIKKR
LETYYKATEPVIAFYEKRGIVRKVNAEGSVDSVFSQVCTHLDALL
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 chain1z83 Chain B Residue 632 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1z83 Crystal structure of human AK1A in complex with AP5A
Resolution1.9 Å
Binding residue
(original residue number in PDB)		P17 G18 S19 G20 K21 G22 T23 T39 G40 L43 R44 M61 Q65 L66 V67 G94 R97 Q101 R128 R132 R138 R149 G177 V179
Binding residue
(residue number reindexed from 1)		P18 G19 S20 G21 K22 G23 T24 T40 G41 L44 R45 M62 Q66 L67 V68 G95 R98 Q102 R129 R133 R139 R150 G178 V180
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K21 R97 R132 R138 R149
Catalytic site (residue number reindexed from 1) K22 R98 R133 R139 R150
Enzyme Commision number 2.7.4.10: nucleoside-triphosphate--adenylate kinase.
2.7.4.3: adenylate kinase.
2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019205 nucleobase-containing compound kinase activity
GO:0047506 (deoxy)adenylate kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006172 ADP biosynthetic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0015949 nucleobase-containing small molecule interconversion
GO:0016310 phosphorylation
GO:0046033 AMP metabolic process
GO:0046034 ATP metabolic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0001520 outer dense fiber
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0036126 sperm flagellum
GO:0070062 extracellular exosome

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Cellular Component
External links
PDB RCSB:1z83, PDBe:1z83, PDBj:1z83
PDBsum1z83
PubMed
UniProtP00568|KAD1_HUMAN Adenylate kinase isoenzyme 1 (Gene Name=AK1)

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