Structure of PDB 6ymh Chain AAA Binding Site BS02

Receptor Information
>6ymh Chain AAA (length=153) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQ
RIVLLIHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIG
KAERLSTLEVSFWGGFRVSLEQIEFWQGGEHRLADRFLYQRENDAWKIDR
LAP
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 chain6ymh Chain BBB Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ymh Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase.
Resolution2.417 Å
Binding residue
(original residue number in PDB)		Q111 W191 R201
Binding residue
(residue number reindexed from 1)		Q95 W126 R136
Annotation score1
Enzymatic activity
Enzyme Commision number 1.4.3.5: pyridoxal 5'-phosphate synthase.
Gene Ontology
Molecular Function
GO:0004733 pyridoxamine phosphate oxidase activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0030170 pyridoxal phosphate binding
GO:0042301 phosphate ion binding
GO:0042803 protein homodimerization activity
GO:1902444 riboflavin binding
Biological Process
GO:0008615 pyridoxine biosynthetic process
GO:0036001 'de novo' pyridoxal 5'-phosphate biosynthetic process
GO:0042816 vitamin B6 metabolic process
GO:0042823 pyridoxal phosphate biosynthetic process
GO:1901615 organic hydroxy compound metabolic process
Cellular Component
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ymh, PDBe:6ymh, PDBj:6ymh
PDBsum6ymh
PubMed34019876
UniProtP0AFI7|PDXH_ECOLI Pyridoxine/pyridoxamine 5'-phosphate oxidase (Gene Name=pdxH)

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