Structure of PDB 3epo Chain B Binding Site BS01

Receptor Information
>3epo Chain B (length=526) Species: 155892 (Caulobacter vibrioides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSTIKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPV
TIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPPEF
PGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDG
EDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKIN
ANIGNTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIG
TVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIP
MTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSL
GDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHK
IKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAM
LCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISR
ARFEFRWEDQFNLGLDPETARKFHDE
Ligand information
Ligand IDMP5
InChIInChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)
InChIKeyPKYFHKIYHBRTPI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1ncc(c(n1)N)COP(=O)(O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(N)n1
ACDLabs 10.04O=P(O)(O)OCc1cnc(nc1N)C
FormulaC6 H10 N3 O4 P
Name(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL DIHYDROGEN PHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain3epo Chain B Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3epo Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y277 H313 S333 R334 G335 R377 E413 L442
Binding residue
(residue number reindexed from 1)		Y255 H291 S311 R312 G313 R355 E391 L420
Annotation score5
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3epo, PDBe:3epo, PDBj:3epo
PDBsum3epo
PubMed18953358
UniProtQ9A6Q5|THIC_CAUVC Phosphomethylpyrimidine synthase (Gene Name=thiC)

[Back to BioLiP]