Structure of PDB 3epn Chain B Binding Site BS01

Receptor Information
>3epn Chain B (length=519) Species: 155892 (Caulobacter vibrioides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIY
DPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVPEFPGRKI
YRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGA
SIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGN
TVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIY
QALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKR
VTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLR
PGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANM
DEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVT
PKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEF
RWEDQFNLGLDPETARKFH
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 chain3epn Chain A Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3epn Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily
Resolution2.11 Å
Binding residue
(original residue number in PDB)		N219 M248 Y277 H313 S333 R334 G335 D374 R377 E413 G414 Y440
Binding residue
(residue number reindexed from 1)		N197 M221 Y250 H286 S306 R307 G308 D347 R350 E386 G387 Y413
Annotation score2
Enzymatic activity
Enzyme Commision number 4.1.99.17: phosphomethylpyrimidine synthase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016829 lyase activity
GO:0016830 carbon-carbon lyase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0070284 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity
Biological Process
GO:0009228 thiamine biosynthetic process
GO:0009229 thiamine diphosphate biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3epn, PDBe:3epn, PDBj:3epn
PDBsum3epn
PubMed18953358
UniProtQ9A6Q5|THIC_CAUVC Phosphomethylpyrimidine synthase (Gene Name=thiC)

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