Structure of PDB 2vi5 Chain F Binding Site BS02

Receptor Information
>2vi5 Chain F (length=147) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DASGVRLAIVASSWHGKICDALLDGARKVAAGCGLDDPTVVRVLGAIEIP
VVAQELARNHDAVVALGVVIRGQTPHFDYVCDAVTQGLTRVSLDSSTPIA
NGVLTTNTEEQALDRAGLPTSAEDKGAQATVAALATALTLRELRAHS
Ligand information
Ligand IDY19
InChIInChI=1S/C12H20N4O7/c1-2-7(20)14-8-10(15-12(23)16-11(8)22)13-3-5(18)9(21)6(19)4-17/h5-6,8-9,17-19,21H,2-4H2,1H3,(H,14,20)(H2,13,15,16,22,23)/t5-,6+,8-,9-/m0/s1
InChIKeyNPNFNBTUUJYCDD-FAYXRDSDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCC(=O)NC1C(=O)NC(=O)N=C1NCC(C(C(CO)O)O)O
ACDLabs 10.04O=C1NC(=O)N=C(NCC(O)C(O)C(O)CO)C1NC(=O)CC
CACTVS 3.341CCC(=O)N[CH]1C(=O)NC(=O)N=C1NC[CH](O)[CH](O)[CH](O)CO
CACTVS 3.341CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@H](O)[C@H](O)[C@H](O)CO
OpenEye OEToolkits 1.5.0CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@@H]([C@@H]([C@@H](CO)O)O)O
FormulaC12 H20 N4 O7
Name1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol
ChEMBL
DrugBank
ZINCZINC000016052607
PDB chain2vi5 Chain J Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vi5 A New Series of N-[2,4-Dioxo-6-D-Ribitylamino-1,2, 3,4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives as Inhibitors of Lumazine Syntase and Riboflavin Synthase: Design, Synthesis, Biochemical Evaluation, Crystallography and Mechanistic Implications.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		A113 N114 A142
Binding residue
(residue number reindexed from 1)		A100 N101 A129
Annotation score1
Binding affinityMOAD: Ki=110uM
Enzymatic activity
Catalytic site (original residue number in PDB) H89
Catalytic site (residue number reindexed from 1) H76
Enzyme Commision number 2.5.1.78: 6,7-dimethyl-8-ribityllumazine synthase.
Gene Ontology
Molecular Function
GO:0000906 6,7-dimethyl-8-ribityllumazine synthase activity
GO:0016740 transferase activity
Biological Process
GO:0009231 riboflavin biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0009349 riboflavin synthase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vi5, PDBe:2vi5, PDBj:2vi5
PDBsum2vi5
PubMed18331058
UniProtP9WHE9|RISB_MYCTU 6,7-dimethyl-8-ribityllumazine synthase (Gene Name=ribH)

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