Structure of PDB 4p3n Chain C Binding Site BS01

Receptor Information
>4p3n Chain C (length=402) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQE
VVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFD
HRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQ
IEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLEN
SLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRF
NLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQV
MVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYN
FILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEE
EF
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 chain4p3n Chain C Residue 800 [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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PDB4p3n Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G387 H388 M411 R442 Y540 T560 D564 L567 H590
Binding residue
(residue number reindexed from 1)		G66 H67 M90 R121 Y219 T239 D243 L246 H269
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C413 R442 Q460 D462 H464 K543 H590
Catalytic site (residue number reindexed from 1) C92 R121 Q139 D141 H143 K222 H269
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4p3n, PDBe:4p3n, PDBj:4p3n
PDBsum4p3n
PubMed25824639
UniProtP26639|SYTC_HUMAN Threonine--tRNA ligase 1, cytoplasmic (Gene Name=TARS1)

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