Structure of PDB 6hdz Chain B Binding Site BS01

Receptor Information
>6hdz Chain B (length=377) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLDPKLVRTQPQEVAARLATRGFQLDVARIEALEEQRKSVQTRDAIQGEL
DAMLLGIPNLPHESVPVGADEDANVEVRRWGTPKTFDFEVKDHVALGERH
GWLDFETAAKLSGARFALMRGPIARLHRALAQFMINLHTAEHGYEEAYTP
YLVQAPALQGTGQLPKFEEDLFKIGRDGEADLYLIPTAEVSLTNIVSGQI
LDAKQLPLKFVAHTPCFRSEAGADTRGMIRQHQFDKVEMVQIVDPATSYE
ALEGLTANAERVLQLLELPYRVLALCTGDMGFGSTKTYDLEVWVPSQDKY
REISSCSNCGDFQARRMQARYRNPETGKPELVHTLNGSGLAVGRTLVAVL
ENYQQADGSIRVPEVLKPYMAGIEVIG
Ligand information
Ligand IDFZK
InChIInChI=1S/C12H18N4O10S/c13-5(3-17)10(21)15-27(23,24)25-4-6-8(19)9(20)11(26-6)16-2-1-7(18)14-12(16)22/h1-2,5-6,8-9,11,17,19-20H,3-4,13H2,(H,15,21)(H,14,18,22)/t5-,6+,8+,9+,11+/m0/s1
InChIKeyQIOFKSOPWDKKDG-DANLAGSESA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH](CO)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 2.0.6C1=CN(C(=O)NC1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(CO)N)O)O
CACTVS 3.385N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 2.0.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O
FormulaC12 H18 N4 O10 S
Name5'-O-(N-(L-seryl)-Sulfamoyl)uridine
ChEMBL
DrugBank
ZINC
PDB chain6hdz Chain B Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hdz Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Resolution2.06 Å
Binding residue
(original residue number in PDB)		T233 E235 R264 Q280 F283 K285 E287 E351 I352 S353 S354 N385 S387 A390 R393
Binding residue
(residue number reindexed from 1)		T187 E189 R218 Q231 F234 K236 E238 E302 I303 S304 S305 N336 S338 A341 R344
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006434 seryl-tRNA aminoacylation
GO:0016260 selenocysteine biosynthetic process
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:6hdz, PDBe:6hdz, PDBj:6hdz
PDBsum6hdz
PubMed31869198
UniProtQ9I0M6|SYS_PSEAE Serine--tRNA ligase (Gene Name=serS)

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