Structure of PDB 3ena Chain B Binding Site BS01

Receptor Information
>3ena Chain B (length=133) Species: 212035 (Acanthamoeba polyphaga mimivirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHY
KEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNTNPLASAPG
TIRGDLANDIGENLIHASDSEDSAVDEISIWFP
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 chain3ena Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3ena Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		H53 Y58 T92 R103 I110 N113
Binding residue
(residue number reindexed from 1)		H53 Y58 T92 R103 I110 N113
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K9 Y50 N113 H116 E127
Catalytic site (residue number reindexed from 1) K9 Y50 N113 H116 E127
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:3ena, PDBe:3ena, PDBj:3ena
PDBsum3ena
PubMed19439473
UniProtQ5UQL3|NDK_MIMIV Nucleoside diphosphate kinase (Gene Name=NDK)

[Back to BioLiP]