Structure of PDB 5vyq Chain B Binding Site BS01

Receptor Information
>5vyq Chain B (length=234) Species: 1310114 (Mycobacterium tuberculosis CAS/NITR204) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QGHMVTILILTDNVHAHALAVDLQARHGDMDVYQSPIGQLPGVPRCDVAE
RVAEIVERYDLVLSFHCKQRFPAALIDGVRCVNVHPGFNPYNRGWFPQVF
SIIDGQKVGVTIHEIDDQLDHGPIIAQRECAIESWDSSGSVYARLMDIER
ELVLEHFDAIRDGSYTAKSPATEGNLNLKKDFEQLRRLDLNERGTFGHFL
NRLRALTHDDFRNAWFVDASGRKVFVRVVLEPEK
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 chain5vyq Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vyq Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		N10 H63 K65 F93 Y139 H205 F208 N210
Binding residue
(residue number reindexed from 1)		N13 H66 K68 F96 Y142 H208 F211 N213
Annotation score2
Enzymatic activity
Enzyme Commision number 2.1.2.-
Gene Ontology
Molecular Function
GO:0004479 methionyl-tRNA formyltransferase activity
GO:0016740 transferase activity
GO:0016742 hydroxymethyl-, formyl- and related transferase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006413 translational initiation
GO:0009058 biosynthetic process
GO:0071951 conversion of methionyl-tRNA to N-formyl-methionyl-tRNA
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vyq, PDBe:5vyq, PDBj:5vyq
PDBsum5vyq
PubMed28665588
UniProtP9WKZ3|SUGFT_MYCTU dTDP-4-amino-4,6-dideoxyglucose formyltransferase (Gene Name=Rv3404c)

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