Structure of PDB 4lbu Chain A Binding Site BS01

Receptor Information
>4lbu Chain A (length=369) Species: 264203 (Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETV
RATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVM
SLSSLTKQSEEGVTFKSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPAT
PSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQS
ADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGK
PDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPL
DSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDS
ISEGRFSQFAQDFRARYFA
Ligand information
Ligand ID1WJ
InChIInChI=1S/C18H24N6O5/c1-20-18-21-9-6-8-11(22-17(19)24-15(8)26)7(12(9)23-18)4-5-10-13(25)14(27-2)16(28-3)29-10/h6,10,13-14,16,25H,4-5H2,1-3H3,(H2,20,21,23)(H3,19,22,24,26)/t10-,13-,14-,16-/m1/s1
InChIKeyXTZFREKGNSFRGQ-DSPGLSBSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CNc1[nH]c2cc3c(c(c2n1)CCC4C(C(C(O4)OC)OC)O)N=C(NC3=O)N
CACTVS 3.385CNc1[nH]c2cc3C(=O)NC(=Nc3c(CC[C@H]4O[C@@H](OC)[C@H](OC)[C@@H]4O)c2n1)N
ACDLabs 12.01O=C1NC(=Nc3c1cc2nc(nc2c3CCC4OC(OC)C(OC)C4O)NC)N
CACTVS 3.385CNc1[nH]c2cc3C(=O)NC(=Nc3c(CC[CH]4O[CH](OC)[CH](OC)[CH]4O)c2n1)N
OpenEye OEToolkits 1.7.6CNc1[nH]c2cc3c(c(c2n1)CC[C@@H]4[C@H]([C@H]([C@@H](O4)OC)OC)O)N=C(NC3=O)N
FormulaC18 H24 N6 O5
Namemethyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-2-O-methyl-beta-D-ribo-hexofuranoside
ChEMBL
DrugBank
ZINCZINC000263621236
PDB chain4lbu Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4lbu Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appended lin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT).
Resolution1.17 Å
Binding residue
(original residue number in PDB)		T47 L68 G69 N70 D102 Y106 Q107 D156 C158 G229 A232 M260 G261 D280
Binding residue
(residue number reindexed from 1)		T38 L59 G60 N61 D93 Y97 Q98 D142 C144 G215 A218 M246 G247 D266
Annotation score1
Binding affinityMOAD: Kd=276nM
PDBbind-CN: -logKd/Ki=6.56,Kd=276nM
Enzymatic activity
Catalytic site (original residue number in PDB) D102 D280 C318 C320 C323 H349
Catalytic site (residue number reindexed from 1) D93 D266 C304 C306 C309 H335
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4lbu, PDBe:4lbu, PDBj:4lbu
PDBsum4lbu
PubMed25483606
UniProtP28720|TGT_ZYMMO Queuine tRNA-ribosyltransferase (Gene Name=tgt)

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