Structure of PDB 2dy9 Chain A Binding Site BS01

Receptor Information
>2dy9 Chain A (length=154) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SETERTLVIIKPDAVVRGLIGEIISRFEKKGLKIVGMKMIWIDRELAEKH
YEEHREKPFFKALIDYITKTPVVVMVLEGRYAVEVVRKMAGATDPKDAAP
GTIRGDFGLEVSDAICNVIHASDSKESAEREISLFFKPEELFEYPRAADW
FYKK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2dy9 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2dy9 Crystal structure of nucleoside diphosphate kinase in complex with ADP
Resolution2.01 Å
Binding residue
(original residue number in PDB)		K15 H58 F63 L67 R91 T97 R108 I119 N121
Binding residue
(residue number reindexed from 1)		K11 H54 F59 L63 R87 T93 R104 I115 N117
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K15 Y55 N121 H124 E135
Catalytic site (residue number reindexed from 1) K11 Y51 N117 H120 E131
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
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:2dy9, PDBe:2dy9, PDBj:2dy9
PDBsum2dy9
PubMed
UniProtO58429|NDK_PYRHO Nucleoside diphosphate kinase (Gene Name=ndk)

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