Structure of PDB 1s59 Chain A Binding Site BS01

Receptor Information
>1s59 Chain A (length=153) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAE
EHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQA
EPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATW
LRE
Ligand information
Ligand IDDGI
InChIInChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyCIKGWCTVFSRMJU-KVQBGUIXSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O10 P2
Name2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL1232205
DrugBankDB03491
ZINCZINC000008215878
PDB chain1s59 Chain A Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1s59 Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling
Resolution2.6 Å
Binding residue
(original residue number in PDB)		F139 R167 T173 T191
Binding residue
(residue number reindexed from 1)		F61 R89 T95 T113
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K91 Y131 N194 H197 E208
Catalytic site (residue number reindexed from 1) K13 Y53 N116 H119 E130
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1s59, PDBe:1s59, PDBj:1s59
PDBsum1s59
PubMed15465053
UniProtO64903|NDK2_ARATH Nucleoside diphosphate kinase II, chloroplastic (Gene Name=NDPK2)

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