Structure of PDB 2v0c Chain A Binding Site BS05

Receptor Information
>2v0c Chain A (length=810) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGKQYVLVMFPYPSGDLHMGHL
KNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYA
NIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAK
GLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERL
LKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTL
FGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKT
GVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARK
FGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIA
WLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELP
VLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFD
SSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFT
KFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRL
EIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVK
EQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALL
ETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLN
ALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAG
WPELDEKALE
Ligand information
Ligand IDANZ
InChIInChI=1S/C17H17BFN5O8P/c19-9-1-2-10-8(3-9)4-28-18(10)31-13-11(5-29-33(25,26)27)30-17(14(13)32-18)24-7-23-12-15(20)21-6-22-16(12)24/h1-3,6-7,11,13-14,17H,4-5H2,(H2,20,21,22)(H2,25,26,27)/q-1/t11-,13-,14-,17-,18+/m1/s1
InChIKeyZLSXXTYLUMEAGG-LBTDBDNISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[B-]12(c3ccc(cc3CO1)F)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)(O)O
OpenEye OEToolkits 1.5.0[B@@-]12(c3ccc(cc3CO1)F)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)(O)O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@H]4O[B-]5(OCc6cc(F)ccc56)O[C@@H]34
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH]4O[B-]5(OCc6cc(F)ccc56)O[CH]34
FormulaC17 H17 B F N5 O8 P
Name[(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYL DIHYDROGEN PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000263621346
PDB chain2v0c Chain A Residue 1817 [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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PDB2v0c An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		F246 T247 T248 R249 V328 L329 Y332 I337 M338 H343 D344
Binding residue
(residue number reindexed from 1)		F243 T244 T245 R246 V325 L326 Y329 I334 M335 H340 D341
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.68,IC50=2.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) F41 H49 H52 D80 C159 C162 F501 H541 F551 V637 K640
Catalytic site (residue number reindexed from 1) F38 H46 H49 D77 C156 C159 F498 H538 F548 V634 K637
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004823 leucine-tRNA ligase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
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:2v0c, PDBe:2v0c, PDBj:2v0c
PDBsum2v0c
PubMed17588934
UniProtQ7SIE4

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