Structure of PDB 2i2d Chain A Binding Site BS01

Receptor Information
>2i2d Chain A (length=255) Species: 1639 (Listeria monocytogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLS
AFHQYEERLDEIAFIGIHTGFYADWRPAEADKLVKLLAKGEYQKVSYPLL
KTTVKYEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPS
GTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVS
LQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVH
DSFIE
Ligand information
Ligand IDA2D
InChIInChI=1S/C20H26N10O13P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(41-19)1-39-44(35,36)43-45(37,38)40-2-8-12(32)14(34)20(42-8)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)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyAKDJDUXNKGWGAZ-XPWFQUROSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[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
ACDLabs 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O
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)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
FormulaC20 H26 N10 O13 P2
NameBIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN DIPHOSPHATE;
BIS(ADENOSINE)-5'-DIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000024852723
PDB chain2i2d Chain A Residue 273 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2i2d NAD kinases use substrate-assisted catalysis for specific recognition of NAD.
Resolution2.22 Å
Binding residue
(original residue number in PDB)
G46 F74 Y75 N122 E123 T161 A162 Y163 S166 H223
Binding residue
(residue number reindexed from 1)
G46 F71 Y72 N114 E115 T153 A154 Y155 S158 H215
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.23: NAD(+) kinase.
Gene Ontology
Molecular Function
GO:0003951 NAD+ kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006741 NADP biosynthetic process
GO:0016310 phosphorylation
GO:0019674 NAD metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:2i2d, PDBe:2i2d, PDBj:2i2d
PDBsum2i2d
PubMed17686780
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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