Structure of PDB 6yhd Chain A Binding Site BS01

Receptor Information
>6yhd Chain A (length=371) 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
SLSSLTKQSEEGVTFKSGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYP
ATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQ
QSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGV
GKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLK
PLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIR
DSISEGRFSQFAQDFRARYFA
Ligand information
Ligand ID1WK
InChIInChI=1S/C17H22N6O5/c1-19-17-20-8-5-7-10(21-16(18)23-14(7)26)6(11(8)22-17)3-4-9-12(24)13(25)15(27-2)28-9/h5,9,12-13,15,24-25H,3-4H2,1-2H3,(H2,19,20,22)(H3,18,21,23,26)/t9-,12-,13-,15-/m1/s1
InChIKeyVKQAJTKFJIETGO-QGMIFYJMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CNc1[nH]c2cc3c(c(c2n1)CC[C@@H]4[C@H]([C@H]([C@@H](O4)OC)O)O)N=C(NC3=O)N
CACTVS 3.385CNc1[nH]c2cc3C(=O)NC(=Nc3c(CC[CH]4O[CH](OC)[CH](O)[CH]4O)c2n1)N
ACDLabs 12.01O=C1NC(=Nc3c1cc2nc(nc2c3CCC4OC(OC)C(O)C4O)NC)N
CACTVS 3.385CNc1[nH]c2cc3C(=O)NC(=Nc3c(CC[C@H]4O[C@@H](OC)[C@H](O)[C@@H]4O)c2n1)N
OpenEye OEToolkits 1.7.6CNc1[nH]c2cc3c(c(c2n1)CCC4C(C(C(O4)OC)O)O)N=C(NC3=O)N
FormulaC17 H22 N6 O5
Namemethyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-beta-D-ribo-hexofuranoside
ChEMBL
DrugBank
ZINCZINC000263621127
PDB chain6yhd 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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PDB6yhd Co-crystallization, nanoESI-MS and 19F NMR reveal dimer disturbing inhibitors and conformational changes at dimer contacts
Resolution1.25 Å
Binding residue
(original residue number in PDB)		L68 N70 D102 Y106 Q107 D156 C158 G229 L231 A232 M260 G261 D280
Binding residue
(residue number reindexed from 1)		L59 N61 D93 Y97 Q98 D144 C146 G217 L219 A220 M248 G249 D268
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D102 D280 C318 C320 C323 H349
Catalytic site (residue number reindexed from 1) D93 D268 C306 C308 C311 H337
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:6yhd, PDBe:6yhd, PDBj:6yhd
PDBsum6yhd
PubMed
UniProtP28720|TGT_ZYMMO Queuine tRNA-ribosyltransferase (Gene Name=tgt)

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