Structure of PDB 1kyy Chain A Binding Site BS01

Receptor Information
>1kyy Chain A (length=149) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESV
PGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRV
GLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL
Ligand information
Ligand IDINI
InChIInChI=1S/C9H14N4O8/c14-2-4(16)6(17)3(15)1-10-7-5(13(20)21)8(18)12-9(19)11-7/h3-4,6,14-17H,1-2H2,(H3,10,11,12,18,19)/t3-,4+,6-/m0/s1
InChIKeyKSKGHNZSCSCHEQ-RPDRRWSUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(C(C(CO)O)O)O)NC1=C(C(=O)NC(=O)N1)[N+](=O)[O-]
OpenEye OEToolkits 1.5.0C([C@@H]([C@@H]([C@@H](CO)O)O)O)NC1=C(C(=O)NC(=O)N1)[N+](=O)[O-]
CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@@H](O)CNC1=C(C(=O)NC(=O)N1)[N+]([O-])=O
ACDLabs 10.04O=C1NC(NCC(O)C(O)C(O)CO)=C(C(=O)N1)[N+]([O-])=O
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)CNC1=C(C(=O)NC(=O)N1)[N+]([O-])=O
FormulaC9 H14 N4 O8
Name5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
ChEMBL
DrugBankDB04162
ZINC
PDB chain1kyy Chain A Residue 201 [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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PDB1kyy 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)		W18 G52 S53 W54 E55 V77 L78 H85
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) H94
Catalytic site (residue number reindexed from 1) H85
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:1kyy, PDBe:1kyy, PDBj:1kyy
PDBsum1kyy
PubMed12083520
UniProtQ9UUB1|RIB4_SCHPO 6,7-dimethyl-8-ribityllumazine synthase (Gene Name=rib4)

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