Structure of PDB 6rkq Chain A Binding Site BS02

Receptor Information
>6rkq 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
SLLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTPA
TSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQS
ADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGK
PDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPL
DSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDS
ISEGRFSQFAQDFRARYFA
Ligand information
Ligand IDK75
InChIInChI=1S/C13H14N6/c1-3-4-8-7-5-10-11(19-13(15-2)18-10)6-9(7)17-12(14)16-8/h5-6,8H,1-2H3,(H3,14,16,17)(H2,15,18,19)/t8-/m1/s1
InChIKeyBBZKTHUVWQCRHC-MRVPVSSYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1[nH]c2cc3N=C(N)N[C@H](C#CC)c3cc2n1
OpenEye OEToolkits 2.0.7CC#C[C@@H]1c2cc3c(cc2N=C(N1)N)[nH]c(n3)NC
CACTVS 3.385CNc1[nH]c2cc3N=C(N)N[CH](C#CC)c3cc2n1
OpenEye OEToolkits 2.0.7CC#CC1c2cc3c(cc2N=C(N1)N)[nH]c(n3)NC
FormulaC13 H14 N6
Name(8~{R})-~{N}2-methyl-8-prop-1-ynyl-7,8-dihydro-3~{H}-imidazo[4,5-g]quinazoline-2,6-diamine
ChEMBL
DrugBank
ZINC
PDB chain6rkq Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rkq Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT.
Resolution1.665 Å
Binding residue
(original residue number in PDB)
D102 Y106 D156 C158 I201 Q203 G229 G230 L231 A232 M260 G261
Binding residue
(residue number reindexed from 1)
D93 Y97 D145 C147 I187 Q189 G215 G216 L217 A218 M246 G247
Annotation score1
Binding affinityMOAD: Ki=48uM
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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Biological Process

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Cellular Component
External links
PDB RCSB:6rkq, PDBe:6rkq, PDBj:6rkq
PDBsum6rkq
PubMed32515955
UniProtP28720|TGT_ZYMMO Queuine tRNA-ribosyltransferase (Gene Name=tgt)

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