Structure of PDB 5zy9 Chain C Binding Site BS01

Receptor Information
>5zy9 Chain C (length=400) Species: 67593 (Phytophthora sojae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDHRRLGVSEELFFFHSLSPGSGFWLPHGSAIYFKLLKFIREQYRARGYT
EVITPNIFNMELWNISGHAKHYKENMFVFDVEGQEYALKPMNCPAASLMF
DFRQRSYRELPIRYADCGVLHRNELSGALTGLTRVRRFQQDDAHIFCRDD
QIKKEVLDFLSFMKYVYDVFGIEFNLELSTRPEKAMGELEQWERAESQLA
EALDEFVGAGKWVVNPGDGAFYGPKIDIMITDALKRQHQCATVQLDFQLP
IRFNLKYRTDDADNFKRPVIIHRAIYGSLERFVAVLVEHYAGKFPFWLSP
RQVLIVTVGAAFVDYGYEVKDAMFRAGFDVDIDDTGKTLNKKIREGQMAH
YNFILVVGAHEKETRSVNIRTRDNKVTGTKTLEEAIAMFKELEETKAADE
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 C Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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 F221 Y222 D246 L249
Binding residue
(residue number reindexed from 1)
G67 H68 M91 R122 F221 Y222 D246 L249
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

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Molecular Function

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Biological Process

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

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