Structure of PDB 4s25 Chain A Binding Site BS02

Receptor Information
>4s25 Chain A (length=513) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPDFQPIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFD
NYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEM
LYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNAN
IGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAV
PVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLR
YIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVA
LSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVP
MHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALG
TALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDA
LSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFC
SMKITEDIRKYAE
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 chain4s25 Chain A Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4s25 Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		N228 M257 Y286 H322 S342 R343 D383 R386 E422 G423 Y449
Binding residue
(residue number reindexed from 1)		N150 M179 Y208 H244 S264 R265 D305 R308 E344 G345 Y371
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4s25, PDBe:4s25, PDBj:4s25
PDBsum4s25
PubMed25813242
UniProtO82392|THIC_ARATH Phosphomethylpyrimidine synthase, chloroplastic (Gene Name=THIC)

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