Structure of PDB 3em1 Chain B Binding Site BS01

Receptor Information
>3em1 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
TIRGDLANDIRENLIHASDSEDSAVDEISIWFP
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 chain3em1 Chain B Residue 143 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3em1 Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		H53 Y58 L62 T92 R103 N113
Binding residue
(residue number reindexed from 1)		H53 Y58 L62 T92 R103 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:3em1, PDBe:3em1, PDBj:3em1
PDBsum3em1
PubMed19439473
UniProtQ5UQL3|NDK_MIMIV Nucleoside diphosphate kinase (Gene Name=NDK)

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