Structure of PDB 6r1m Chain B Binding Site BS01

Receptor Information
>6r1m Chain B (length=428) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLDPNLLRNEPDAVAEKLARRGFKLDVDKLGALEERRKVLQVKTENLQAE
RNSRSKSIGQAKARGEDIEPLRLEVNKLGEELDAAKAELDALQAEIRDIA
LTIPNLPADEVPVGKDENDNVEVSRWGTPREFDFEVRDHVTLGEMHSGLD
FAAAVKLTGSRFVVMKGQIARMHRALSQFMLDLHTEQHGYSENYVPYLVN
QDTLYGTGQLPKFAGDLFHTRPLEEEADTSNYALIPTAEVPLTNLVRGEI
IDEDDLPIKMTAHTPCFRSEAGSYGRDTRGLIRMHQFDKVEMVQIVRPED
SMAALEEMTGHAEKVLQLLGLPYRKIILCTGDMGFGACKTYDLEVWIPAQ
NTYREISSCSNVWDFQARRMQARCRSKKKTRLVHTLNGSGLAVGRTLVAV
MENYQQADGRIEVPEVLRPYMNGLEYIG
Ligand information
Ligand IDSSA
InChIInChI=1S/C13H19N7O8S/c14-5(1-21)12(24)19-29(25,26)27-2-6-8(22)9(23)13(28-6)20-4-18-7-10(15)16-3-17-11(7)20/h3-6,8-9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,8+,9+,13+/m0/s1
InChIKeyHQXFJGONGJPTLZ-YTMOPEAISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O)N
CACTVS 3.341N[CH](CO)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CO)N)O)O)N
FormulaC13 H19 N7 O8 S
Name5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163070
DrugBankDB03869
ZINCZINC000013542770
PDB chain6r1m Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6r1m Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		T237 E239 R268 E270 I282 R283 M284 F287 K289 E291 E355 I356 S357 S358 N389 S391 A394 R397
Binding residue
(residue number reindexed from 1)		T237 E239 R268 E270 I282 R283 M284 F287 K289 E291 E355 I356 S357 S358 N387 S389 A392 R395
Annotation score2
Binding affinityMOAD: ic50=0.21uM
BindingDB: IC50=210nM,Kd=1.3nM,Ki=0.180000nM
Enzymatic activity
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005524 ATP binding
GO:0042802 identical protein 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
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:6r1m, PDBe:6r1m, PDBj:6r1m
PDBsum6r1m
PubMed31626547
UniProtP0A8L1|SYS_ECOLI Serine--tRNA ligase (Gene Name=serS)

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