Structure of PDB 1kyv Chain A Binding Site BS01

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 A Residue 501 [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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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)		W27 G61 S62 W63 E64 V86 L87 H94
Binding residue
(residue number reindexed from 1)		W16 G50 S51 W52 E53 V75 L76 H83
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
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Biological Process
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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)

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