Structure of PDB 5zy9 Chain E Binding Site BS01

Receptor Information
>5zy9 Chain E (length=398) Species: 67593 (Phytophthora sojae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HRRLGVSEELFFFHSLSPGSGFWLPHGSAIYFKLLKFIREQYRARGYTEV
ITPNIFNMELWNISGHAKHYKENMFVFDVEGQEYALKPMNCPAASLMFDF
RQRSYRELPIRYADCGVLHRNELSGALTGLTRVRRFQQDDAHIFCRDDQI
KKEVLDFLSFMKYVYDVFGIEFNLELSTRPEKAMGELEQWERAESQLAEA
LDEFVGAGKWVVNPGDGAFYGPKIDIMITDALKRQHQCATVQLDFQLPIR
FNLKYRTDDADNFKRPVIIHRAIYGSLERFVAVLVEHYAGKFPFWLSPRQ
VLIVTVGAAFVDYGYEVKDAMFRAGFDVDIDDTGKTLNKKIREGQMAHYN
FILVVGAHEKETRSVNIRTRDNKVTGTKTLEEAIAMFKELEETKAADE
Ligand information
Ligand ID2CR
InChIInChI=1S/C28H43NO6/c1-17-12-18(2)14-20(4)27(32)21(16-29)8-5-6-11-25(22-9-7-10-23(22)28(33)34)35-26(31)15-24(30)19(3)13-17/h5-6,8,17-20,22-25,27,30,32H,7,9-15H2,1-4H3,(H,33,34)/b6-5+,21-8+/t17-,18+,19-,20-,22+,23+,24-,25-,27+/m0/s1
InChIKeyOJCKRNPLOZHAOU-RSXXJMTFSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1C[C@@H](C)C[C@H](C)[C@@H](O)C(=C/C=C/C[C@H](OC(=O)C[C@H](O)[C@@H](C)C1)[C@@H]2CCC[C@H]2C(O)=O)/C#N
OpenEye OEToolkits 1.9.2C[C@H]1C[C@H](C[C@@H]([C@H](/C(=C/C=C/C[C@H](OC(=O)C[C@@H]([C@H](C1)C)O)[C@@H]2CCC[C@H]2C(=O)O)/C#N)O)C)C
CACTVS 3.385C[CH]1C[CH](C)C[CH](C)[CH](O)C(=CC=CC[CH](OC(=O)C[CH](O)[CH](C)C1)[CH]2CCC[CH]2C(O)=O)C#N
OpenEye OEToolkits 1.9.2CC1CC(CC(C(C(=CC=CCC(OC(=O)CC(C(C1)C)O)C2CCCC2C(=O)O)C#N)O)C)C
ACDLabs 12.01O=C(O)C1CCCC1C2OC(=O)CC(O)C(C)CC(C)CC(C)CC(C(O)C(C#N)=CC=CC2)C
FormulaC28 H43 N O6
Name(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid;
Borrelidin
ChEMBL
DrugBank
ZINCZINC000136460740
PDB chain5zy9 Chain E Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5zy9 Structural basis for inhibition of translational functions on a tRNA synthetase
Resolution2.5 Å
Binding residue
(original residue number in PDB)
G67 H68 M91 R122 Y222 D246 H272
Binding residue
(residue number reindexed from 1)
G65 H66 M89 R120 Y220 D244 H270
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.3: threonine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004829 threonine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006435 threonyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5zy9, PDBe:5zy9, PDBj:5zy9
PDBsum5zy9
PubMed
UniProtG3FIN0

[Back to BioLiP]