Structure of PDB 2vi5 Chain B Binding Site BS02

Receptor Information
>2vi5 Chain B (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 B 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)		W27 G58 A59 I60 E61 V81 V82 I83
Binding residue
(residue number reindexed from 1)		W14 G45 A46 I47 E48 V68 V69 I70
Annotation score1
Binding affinityMOAD: Ki=110uM
PDBbind-CN: -logKd/Ki=3.96,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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