Structure of PDB 1kyv Chain A Binding Site BS02

Receptor Information
>1kyv Chain A (length=147) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPG
SWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGL
DSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL
Ligand information
Ligand IDRBF
InChIInChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1
InChIKeyAUNGANRZJHBGPY-SCRDCRAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO)c2cc1C
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO)O)O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)CO
FormulaC17 H20 N4 O6
NameRIBOFLAVIN;
RIBOFLAVINE;
VITAMIN B2
ChEMBLCHEMBL1534
DrugBankDB00140
ZINCZINC000002036848
PDB chain1kyv Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1kyv The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I118 L119 H142 W146
Binding residue
(residue number reindexed from 1)		I107 L108 H131 W135
Annotation score2
Binding affinityMOAD: Kd=1.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) H94
Catalytic site (residue number reindexed from 1) H83
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:0004746 riboflavin synthase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:1902444 riboflavin binding
Biological Process
GO:0009231 riboflavin biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
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:1kyv, PDBe:1kyv, PDBj:1kyv
PDBsum1kyv
PubMed12083520
UniProtQ9UUB1|RIB4_SCHPO 6,7-dimethyl-8-ribityllumazine synthase (Gene Name=rib4)

[Back to BioLiP]