Structure of PDB 3sm0 Chain A Binding Site BS02

Receptor Information
>3sm0 Chain A (length=364) Species: 542 (Zymomonas mobilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVR
ATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMS
LTKQSEEGVTFKSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRA
ASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADAL
AEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDI
VGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSEC
HCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEG
RFSQFAQDFRARYF
Ligand information
Ligand IDAEK
InChIInChI=1S/C18H24N6O/c1-19-18-23-14-8-13-15(21-10-22-17(13)25)12(16(14)24-18)6-7-20-9-11-4-2-3-5-11/h8,10-11,20H,2-7,9H2,1H3,(H2,19,23,24)(H,21,22,25)
InChIKeyIEHXPXUWCFKZTR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CNc1[nH]c2c(CCNCC3CCCC3)c4N=CNC(=O)c4cc2n1
OpenEye OEToolkits 1.7.2CNc1[nH]c2c(n1)cc3c(c2CCNCC4CCCC4)N=CNC3=O
ACDLabs 12.01O=C2c3cc1nc(NC)nc1c(c3N=CN2)CCNCC4CCCC4
FormulaC18 H24 N6 O
Name4-{2-[(cyclopentylmethyl)amino]ethyl}-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ChEMBL
DrugBank
ZINCZINC000095921405
PDB chain3sm0 Chain A Residue 501 [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]
PDB3sm0 From lin-Benzoguanines to lin-Benzohypoxanthines as Ligands for Zymomonas mobilis tRNA-Guanine Transglycosylase: Replacement of Protein-Ligand Hydrogen Bonding by Importing Water Clusters.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		V45 N70 D102 Y106 Q107 D156 C158 G229 A232 M260 G261 D280
Binding residue
(residue number reindexed from 1)		V35 N60 D92 Y96 Q97 D138 C140 G211 A214 M242 G243 D262
Annotation score1
Binding affinityMOAD: Ki=740nM
PDBbind-CN: -logKd/Ki=6.13,Ki=740nM
Enzymatic activity
Catalytic site (original residue number in PDB) D102 D280 C318 C320 C323 H349
Catalytic site (residue number reindexed from 1) D92 D262 C300 C302 C305 H331
Enzyme Commision number 2.4.2.29: tRNA-guanosine(34) preQ1 transglycosylase.
Gene Ontology
Molecular Function
GO:0008479 tRNA-guanosine(34) queuine transglycosylase activity
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0002099 tRNA wobble guanine modification
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0008616 queuosine biosynthetic process
GO:0101030 tRNA-guanine transglycosylation
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:3sm0, PDBe:3sm0, PDBj:3sm0
PDBsum3sm0
PubMed22736391
UniProtP28720|TGT_ZYMMO Queuine tRNA-ribosyltransferase (Gene Name=tgt)

[Back to BioLiP]