Structure of PDB 4s26 Chain A Binding Site BS02

Receptor Information
>4s26 Chain A (length=519) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSSPDFQPIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPA
FDNYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITE
EMLYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVN
ANIGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNS
AVPVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVL
LRYIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYD
VALSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGH
VPMHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGA
LGTALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWD
DALSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPK
FCSMKITEDIRKYAEENGY
Ligand information
Ligand IDIRN
InChIInChI=1S/C8H13N2O7P/c11-6-5(3-16-18(13,14)15)17-8(7(6)12)10-2-1-9-4-10/h1-2,4-8,11-12H,3H2,(H2,13,14,15)/t5-,6-,7-,8-/m1/s1
InChIKeyYEBULYOZZUNFGU-WCTZXXKLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2ccnc2
OpenEye OEToolkits 1.5.0c1cn(cn1)C2C(C(C(O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0c1cn(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccnc2
ACDLabs 10.04O=P(O)(O)OCC2OC(n1cncc1)C(O)C2O
FormulaC8 H13 N2 O7 P
Name1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole
ChEMBL
DrugBank
ZINCZINC000058650251
PDB chain4s26 Chain A Residue 702 [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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PDB4s26 Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		N228 M257 Y286 H322 S342 R343 G344 D383 R386 E422 G423 L451
Binding residue
(residue number reindexed from 1)		N152 M181 Y210 H246 S266 R267 G268 D307 R310 E346 G347 L375
Annotation score2
Enzymatic activity
Enzyme Commision number 4.1.99.17: phosphomethylpyrimidine synthase.
Gene Ontology
Molecular Function
GO:0016830 carbon-carbon lyase activity
GO:0051536 iron-sulfur cluster binding
Biological Process
GO:0009228 thiamine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4s26, PDBe:4s26, PDBj:4s26
PDBsum4s26
PubMed25813242
UniProtO82392|THIC_ARATH Phosphomethylpyrimidine synthase, chloroplastic (Gene Name=THIC)

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