Structure of PDB 1ejb Chain E Binding Site BS02

Receptor Information
>1ejb Chain E (length=168) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEEN
NIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEY
ISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGE
DWGAAAVEMAVKFGKNAF
Ligand information
Ligand IDINJ
InChIInChI=1S/C14H26N3O9P/c18-7-10(20)11(21)9(19)6-15-12-8(13(22)17-14(23)16-12)4-2-1-3-5-27(24,25)26/h9-11,18-21H,1-7H2,(H2,24,25,26)(H3,15,16,17,22,23)/t9-,10+,11-/m0/s1
InChIKeyBMATWAHJJFXMFA-AXFHLTTASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CCc1c(nc(nc1O)O)NCC(C(C(CO)O)O)O)CCP(=O)(O)O
OpenEye OEToolkits 1.5.0C(CCc1c(nc(nc1O)O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O)CCP(=O)(O)O
ACDLabs 10.04O=P(O)(O)CCCCCc1c(O)nc(O)nc1NCC(O)C(O)C(O)CO
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)CNc1nc(O)nc(O)c1CCCCC[P](O)(O)=O
CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@@H](O)CNc1nc(O)nc(O)c1CCCCC[P](O)(O)=O
FormulaC14 H26 N3 O9 P
Name5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC ACID
ChEMBL
DrugBankDB04266
ZINCZINC000003871086
PDB chain1ejb Chain E Residue 800 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1ejb The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		W26 G59 S60 Y61 E62 V89 L90 I91 G93 S94 T95
Binding residue
(residue number reindexed from 1)		W26 G59 S60 Y61 E62 V89 L90 I91 G93 S94 T95
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H97
Catalytic site (residue number reindexed from 1) H97
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:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0009349 riboflavin synthase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ejb, PDBe:1ejb, PDBj:1ejb
PDBsum1ejb
PubMed10860731
UniProtP50861|RIB4_YEAST 6,7-dimethyl-8-ribityllumazine synthase (Gene Name=RIB4)

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