Structure of PDB 4l87 Chain A Binding Site BS01

Receptor Information
>4l87 Chain A (length=476) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRAD
NLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVS
QIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDV
DNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLV
FLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVI
GKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCF
RQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEF
YQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDY
QARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGIT
VPEKLKEFMPPGLQELIPFVKPAPIE
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 chain4l87 Chain A Residue 501 [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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PDB4l87 Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes.
Resolution2.897 Å
Binding residue
(original residue number in PDB)		T271 R302 E304 F316 V318 F321 K323 E325 E391 L392 V393 S394 N427 T429 A432 R435
Binding residue
(residue number reindexed from 1)		T270 R301 E303 F315 V317 F320 K322 E324 E390 L391 V392 S393 N426 T428 A431 R434
Annotation score2
Binding affinityBindingDB: IC50=2170nM
Enzymatic activity
Catalytic site (original residue number in PDB) R302 R317 E391 S394 R435
Catalytic site (residue number reindexed from 1) R301 R316 E390 S393 R434
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0019899 enzyme binding
GO:0042803 protein homodimerization activity
GO:0060090 molecular adaptor activity
GO:0098619 selenocysteine-tRNA ligase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001514 selenocysteine incorporation
GO:0002181 cytoplasmic translation
GO:0006400 tRNA modification
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006434 seryl-tRNA aminoacylation
GO:0016525 negative regulation of angiogenesis
GO:1904046 negative regulation of vascular endothelial growth factor production
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4l87, PDBe:4l87, PDBj:4l87
PDBsum4l87
PubMed24095058
UniProtP49591|SYSC_HUMAN Serine--tRNA ligase, cytoplasmic (Gene Name=SARS1)

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