Structure of PDB 6pup Chain A Binding Site BS03

Receptor Information
>6pup Chain A (length=169) Species: 402676 (Schizosaccharomyces japonicus yFS275) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDISACSINIFYSTLGGSTQKFAEHVADRIRSSLQTELVEILNLDYIDLD
EYFSKGNSNTVYLVLLPSYAIESSIDYFLSALQTTIDDFRIVARPLEKLR
GFAVLGFGDFEQYAGDLFCYQAIAADQRLAKLGAQRIAPLGVVNVKLEKA
QVYEAMEAWTDLFLQYAKE
Ligand information
Ligand IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain6pup Chain A Residue 303 [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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PDB6pup Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		T94 L95 G96 S98 T99 P147 S148 Y149 A150 G188 D189 Y193 L197 F198 V225
Binding residue
(residue number reindexed from 1)		T14 L15 G16 S18 T19 P67 S68 Y69 A70 G108 D109 Y113 L117 F118 V145
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.3.44: tRNA 4-demethylwyosine synthase (AdoMet-dependent).
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0010181 FMN binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0008033 tRNA processing

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pup, PDBe:6pup, PDBj:6pup
PDBsum6pup
PubMed35693892
UniProtB6K6D6

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