Structure of PDB 3nm3 Chain D Binding Site BS02

Receptor Information
>3nm3 Chain D (length=511) Species: 5478 (Nakaseomyces glabratus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KFSKEQFDYSLYLVTDSGMIPEGKTLYGQVEAGLQNGVTLVQIREKDADT
KFFIEEALQIKELCHAHNVPLIINDRIDVAMAIGADGIHVGQDDMPIPMI
RKLVGPDMVIGWSVGFPEEVDELSKMGPDMVDYIGVGTLFPTLTKKNKKM
GTAGAIRVLDALERNNAHWCRTVGIGGLHPDNIERVLYQCVSSNGKRSLD
GICVVSDIIASLDAAKSTKILRGLIDKTDYKFVNIGLSTKNSLTTTDEIQ
SIISNTLKARPLVQHITNKVHQNFGANVTLALGSSPIMSEIQSEVNDLAA
IPHATLLLNTGSVAPPEMLKAAIRAYNDVKRPIVFDPVGATETRLLLNNK
LLTFGQFSCIKGNSSEILGLAELSNELLIQATKIVAFKYKTVAVCTGEFD
FIADGTIEGKYSLSKGTNGTSVEDIPCVAVEAGPIGCSLGSTIACMIGGQ
PSEGNLFHAVVAGVMLYKAAGKIASEKCNGSGSFQVELIDALYRLTRENT
PVTWAPKLTHT
Ligand information
Ligand IDTPS
InChIInChI=1S/C12H17N4O4PS/c1-8-11(3-4-20-21(17,18)19)22-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H3-,13,14,15,17,18,19)/p+1
InChIKeyHZSAJDVWZRBGIF-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H18 N4 O4 P S
NameTHIAMIN PHOSPHATE
ChEMBLCHEMBL1236378
DrugBank
ZINCZINC000001532839
PDB chain3nm3 Chain D Residue 2004 [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]
PDB3nm3 Domain Organization in Candida glabrata THI6, a Bifunctional Enzyme Required for Thiamin Biosynthesis in Eukaryotes .
Resolution3.102 Å
Binding residue
(original residue number in PDB)
Q43 R45 H90 S114 T143 T145 I179 G180 G181 V209 S210
Binding residue
(residue number reindexed from 1)
Q42 R44 H89 S113 T142 T144 I175 G176 G177 V205 S206
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R45 S114 K146
Catalytic site (residue number reindexed from 1) R44 S113 K145
Enzyme Commision number 2.5.1.3: thiamine phosphate synthase.
2.7.1.50: hydroxyethylthiazole kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004417 hydroxyethylthiazole kinase activity
GO:0004789 thiamine-phosphate diphosphorylase activity
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009228 thiamine biosynthetic process
GO:0009229 thiamine diphosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:3nm3, PDBe:3nm3, PDBj:3nm3
PDBsum3nm3
PubMed20968298
UniProtQ6FV03

[Back to BioLiP]