Structure of PDB 5j9n Chain A Binding Site BS02

Receptor Information
>5j9n Chain A (length=368) 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
LSKQSEEGVTFKSHGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATP
SRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSA
DALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKP
DDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLD
SECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSI
SEGRFSQFAQDFRARYFA
Ligand information
Ligand ID6H9
InChIInChI=1S/C9H11N5O/c1-11-9-12-6-3-2-5(8(15)14-10)4-7(6)13-9/h2-4H,10H2,1H3,(H,14,15)(H2,11,12,13)
InChIKeyUAYYHYYNSIPFPB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c2(nc1c(cc(cc1)C(=O)NN)n2)NC
CACTVS 3.385
OpenEye OEToolkits 2.0.4		CNc1[nH]c2ccc(cc2n1)C(=O)NN
FormulaC9 H11 N5 O
Name2-(methylamino)-1H-benzimidazole-5-carbohydrazide
ChEMBLCHEMBL4639064
DrugBank
ZINC
PDB chain5j9n Chain A Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5j9n Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines.
Resolution1.64 Å
Binding residue
(original residue number in PDB)		Y106 D156 C158 I201 Q203 A232 M260 G261
Binding residue
(residue number reindexed from 1)		Y96 D141 C143 I186 Q188 A217 M245 G246
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D102 D280 C318 C320 C323 H349
Catalytic site (residue number reindexed from 1) D92 D265 C303 C305 C308 H334
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:5j9n, PDBe:5j9n, PDBj:5j9n
PDBsum5j9n
PubMed
UniProtP28720|TGT_ZYMMO Queuine tRNA-ribosyltransferase (Gene Name=tgt)

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