Structure of PDB 6fmn Chain A Binding Site BS02

Receptor Information
>6fmn Chain A (length=373) 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]
RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVR
ATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMS
LSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTP
YPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENL
RQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLM
GVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSED
LKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQK
IRDSISEGRFSQFAQDFRARYFA
Ligand information
Ligand IDE4E
InChIInChI=1S/C15H18N6O5/c1-25-13-11(23)10(22)9(26-13)4-17-15-19-7-2-5-6(3-8(7)20-15)18-14(16)21-12(5)24/h2-3,9-11,13,22-23H,4H2,1H3,(H2,17,19,20)(H3,16,18,21,24)/t9-,10-,11-,13-/m1/s1
InChIKeyORQGUYZIZOFXKV-PRULPYPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COC1C(C(C(O1)CNc2[nH]c3cc4c(cc3n2)C(=O)NC(=N4)N)O)O
OpenEye OEToolkits 2.0.6CO[C@H]1[C@@H]([C@@H]([C@H](O1)CNc2[nH]c3cc4c(cc3n2)C(=O)NC(=N4)N)O)O
CACTVS 3.385CO[CH]1O[CH](CNc2[nH]c3cc4N=C(N)NC(=O)c4cc3n2)[CH](O)[CH]1O
CACTVS 3.385CO[C@@H]1O[C@H](CNc2[nH]c3cc4N=C(N)NC(=O)c4cc3n2)[C@@H](O)[C@H]1O
FormulaC15 H18 N6 O5
Name6-azanyl-2-[[(2~{R},3~{S},4~{R},5~{R})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-3,7-dihydroimidazo[4,5-g]quinazolin-8-one
ChEMBL
DrugBank
ZINC
PDB chain6fmn Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fmn Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase.
Resolution1.36 Å
Binding residue
(original residue number in PDB)
D102 Y106 D156 C158 G229 L231 A232 M260 G261
Binding residue
(residue number reindexed from 1)
D92 Y96 D146 C148 G219 L221 A222 M250 G251
Annotation score1
Binding affinityMOAD: Kd=1120nM
PDBbind-CN: -logKd/Ki=5.95,Kd=1120nM
Enzymatic activity
Catalytic site (original residue number in PDB) D102 D280 C318 C320 C323 H349
Catalytic site (residue number reindexed from 1) D92 D270 C308 C310 C313 H339
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:6fmn, PDBe:6fmn, PDBj:6fmn
PDBsum6fmn
PubMed29939431
UniProtP28720|TGT_ZYMMO Queuine tRNA-ribosyltransferase (Gene Name=tgt)

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