Structure of PDB 3g2x Chain F Binding Site BS01

Receptor Information
>3g2x Chain F (length=132) Species: 212035 (Acanthamoeba polyphaga mimivirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYK
EHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNTNPLASAPGT
IRGDLANDIRENLIHASDSEDSAVDEISIWFP
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain3g2x Chain F Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3g2x Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		H53 Y58 R86 T92 R103 I110 R111
Binding residue
(residue number reindexed from 1)		H52 Y57 R85 T91 R102 I109 R110
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K9 Y50 N113 H116 E127
Catalytic site (residue number reindexed from 1) K8 Y49 N112 H115 E126
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3g2x, PDBe:3g2x, PDBj:3g2x
PDBsum3g2x
PubMed19439473
UniProtQ5UQL3|NDK_MIMIV Nucleoside diphosphate kinase (Gene Name=NDK)

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