Structure of PDB 5k1k Chain A Binding Site BS01

Receptor Information
>5k1k Chain A (length=347) Species: 211586 (Shewanella oneidensis MR-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVENLFDTYKLNDTITLKNRILMAPLTRCMADANLVPTDDMVAYYARRAE
AGLIISEATIIRPDAQGYPNTPGIFTQAQIAGWRKVTDAVHANGGKIFVQ
LWHTGRVAHPHFFGGGDVLAPSAQKIEGSVPRMRELTYVTPKAVTVEDIQ
GLVRDYAKAAENVIEAGFDGVEIHGANGYLIDQFLHHDSNRRTDEYGGTP
VNMSRFALEVVDAIIARIGHDRTGLRISPGAYFNMASDSRDRVVFDYLLP
ELEKRDLAFVHIGIFDDSIEFDYLGGTASSYVRAHYGKTLVGVGSYSAET
ASKAIAEDKFDLIAIGRPFIANPDYVAKVRNSEELVAYSDEMLASLI
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 chain5k1k Chain A Residue 401 [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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PDB5k1k Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.
Resolution1.301 Å
Binding residue
(original residue number in PDB)		P33 L34 T35 A66 Q108 H182 N185 R234 I272 F273 V301 G302 S303 G324 R325 L351
Binding residue
(residue number reindexed from 1)		P25 L26 T27 A58 Q100 H174 N177 R226 I264 F265 V293 G294 S295 G316 R317 L343
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T35 H182 N185 Y187 R234 N242 D275
Catalytic site (residue number reindexed from 1) T27 H174 N177 Y179 R226 N234 D267
Enzyme Commision number 1.5.1.30: flavin reductase (NADPH).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0042602 riboflavin reductase (NADPH) activity
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5k1k, PDBe:5k1k, PDBj:5k1k
PDBsum5k1k
PubMed28869767
UniProtQ8EBV3

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