Structure of PDB 8wnj Chain A Binding Site BS02

Receptor Information
>8wnj Chain A (length=917) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EYKDTLNLNTTTFSMKGNLSVNEPKTYAKWQEQQAFKRMQARKDNHGDFT
LHDGPPYANGHLHLGHALNKILKDIVVKREYFKGKKIYYTPGWDCHGLPI
EQQILERLEKEKTSLENPTLFREKCRDHAKKFLEIQKNEFLQLGVLGDFE
DPYKTMDFKFEASIYRALVEVAKKGLLKERHKPIYWSYACESALAEAEVE
YKMKKSPSIFVAFGLKKESLEKLKVKKASLVIWTTTPWTLYANVAIALKK
DAVYALTQKGYLVAKALHEKLAALGVVDNEITHEFNSNDLEYLVATNPLN
QRDSLVALGEHVGLEDGTGAVHTAPGHGEEDYYLGLRYNLEVLMSVDEKG
CYDEGIIHNQLLDESYLGEHVFKAQKRIIEQLGDSLLLEQEIEHSYPHCW
RTHKPVIYRATTQWFILMDEPFIQNDGSQKTLREVALDAIEKVEFVPSSG
KNRLKTMIENRPDWCLSRQRKWGVPLAFFIDKRTNKPCFESEVLEHVANL
FEKKGCDVWWEYSVKDLLPPSYQEDAKHYEKIMHILDVWFDSGSTFKAVL
EDYHGEKGQSPSDVILEGSDQHRGWFQSSLLIGCVLNNQAPFKKVITHGF
IVDEKGEKMSKSKGNVVSLDKLLKTHGSDVVRLWVAFNDYQNDLRVSQTF
FTQTEQHYKKFRNTLKFLLANFSDMDLKNLERPHNFSPLDHFMLETLETI
SAGVNSAFEEHDFVKGLNILMAFVTNELSGIYLDACKDSLYCDSKNNEKR
QAIQMVLLATASKLCYFLAPILTHTIEEVLEHSQALRIFLQAKDVFDLKD
ISVSEKLHLKEFKKPENFEAVLALRSAFNEELDRLKKEGVIKNSLECAIE
VKEKALDENLVEELLMVSFVGIAKEKLSETPAFTLFKAPFYKCPRCWRFK
SELENTPCKRCEQVLKE
Ligand information
Ligand IDGV6
InChIInChI=1S/C16H25N6O8P/c1-3-7(2)9(17)16(25)30-31(26,27)28-4-8-11(23)12(24)15(29-8)22-6-21-10-13(18)19-5-20-14(10)22/h5-9,11-12,15,23-24H,3-4,17H2,1-2H3,(H,26,27)(H2,18,19,20)/t7-,8+,9-,11+,12+,15+/m0/s1
InChIKeyACZWYNUJBRLCEC-XATJSACLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC(C)C(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
OpenEye OEToolkits 2.0.7CC[C@H](C)[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.385CC[C@H](C)[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
CACTVS 3.385CC[CH](C)[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC16 H25 N6 O8 P
Name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate
ChEMBL
DrugBank
ZINC
PDB chain8wnj Chain A Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8wnj Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		P57 Y59 H65 G67 D96 W541 S544 E569 G570 Q573 F602 I603
Binding residue
(residue number reindexed from 1)		P55 Y57 H63 G65 D94 W539 S542 E567 G568 Q571 F600 I601
Annotation score3
Enzymatic activity
Enzyme Commision number 6.1.1.5: isoleucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004822 isoleucine-tRNA ligase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006428 isoleucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8wnj, PDBe:8wnj, PDBj:8wnj
PDBsum8wnj
PubMed38246751
UniProtP56456|SYI_HELPY Isoleucine--tRNA ligase (Gene Name=ileS)

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