Structure of PDB 4rqf Chain A Binding Site BS02

Receptor Information
>4rqf Chain A (length=451) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRAD
NLNKLKNLCSKTIFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIK
LEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDL
VVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPI
YTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSE
QPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEK
IEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAA
SKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTMMDKVEFVHM
LNATMCATTRTICAILENYQTKKGITVPEKLKEFMPPGLQELIPFVKPAP
I
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain4rqf Chain A Residue 602 [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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PDB4rqf SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis.
Resolution3.503 Å
Binding residue
(original residue number in PDB)		R317 V318 F321 L392 S394 A432 R435
Binding residue
(residue number reindexed from 1)		R294 V295 F298 L369 S371 A407 R410
Annotation score3
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: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:4rqf, PDBe:4rqf, PDBj:4rqf
PDBsum4rqf
PubMed26433229
UniProtP49591|SYSC_HUMAN Serine--tRNA ligase, cytoplasmic (Gene Name=SARS1)

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