Structure of PDB 6rlv Chain A Binding Site BS01

Receptor Information
>6rlv Chain A (length=454) Species: 31285 (Trypanosoma brucei gambiense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVLDIQLFRDETGANIIRESQRRRFADPDIVDAIIEADKKWRRTQFLTEA
SKKLINICSKAVGAKKKAKEADGDTSEIPPQVKEAYENGTLKGEQVEQLC
VLQLKQLSKDLSDQVAGLAKEAQQLEEERDKLMLNVGNILHESVPIAQDE
ETGNTVVRTFGNTTKRAKLNHVSIMERLGMMDTSKAVTSMAGGRSYVLKG
GLVQLQVALVSYSLDFLVKRGYTPFYPPFFLNRDVMGEVAQLSQFDEELY
QVSGDKKYLIATSEMPIAAYHRGRWFTELKEPLKYAGMSTCFRKEALGIF
RVHQFDKIEQFVVCSPRQEESWRHLEDMITTSEEFNKSLGLPYRVVNICS
GALNNAAAKKYDLEAWFPASGAFRELVSCSNCTDYQSQSVNCRYGPNLRG
TAAVKEYCHMLNGTLCAITRTMCCICENYQTEEGVVIPDVLRPYMMGIEM
IRFE
Ligand information
Ligand IDFZT
InChIInChI=1S/C13H20N4O10S/c1-16-8(19)2-3-17(13(16)23)12-10(21)9(20)7(27-12)5-26-28(24,25)15-11(22)6(14)4-18/h2-3,6-7,9-10,12,18,20-21H,4-5,14H2,1H3,(H,15,22)/t6-,7+,9+,10+,12+/m0/s1
InChIKeyFDYLXUQGMZNPQQ-IXKMEIRJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)CO)[CH](O)[CH]2O)C1=O
CACTVS 3.385CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)CO)[C@@H](O)[C@H]2O)C1=O
OpenEye OEToolkits 2.0.6CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(CO)N)O)O
OpenEye OEToolkits 2.0.6CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O
FormulaC13 H20 N4 O10 S
Name5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine
ChEMBL
DrugBank
ZINC
PDB chain6rlv Chain A Residue 507 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rlv Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		T264 E266 R295 E297 R310 V311 F314 E318 E384 L385 V386 S387 N423 T425 A428 R431
Binding residue
(residue number reindexed from 1)		T262 E264 R293 E295 R301 V302 F305 E309 E375 L376 V377 S378 N412 T414 A417 R420
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006434 seryl-tRNA aminoacylation
Cellular Component
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:6rlv, PDBe:6rlv, PDBj:6rlv
PDBsum6rlv
PubMed31869198
UniProtD0A7P1

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