Structure of PDB 6trq Chain A Binding Site BS01

Receptor Information
>6trq Chain A (length=332) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFASLIKRFQFVSVLDSNPQTKVMSLLGTIDNKDAIITAEKTHFLFDETD
GRSTPVLYNCENEYSCINGIQELKEITSNDIYYWGLSVIKQDMESNPTAK
LNLIWPATPIHIKKYEQQNFHLVRETPEMYKRIVQPYIEEMCNNGRLKWV
NNILYEGAESERVVYKDFSEKDDGFLILPDMKWDGMNLDSLYLVAIVYRT
DIKTIRDLRYSDRQWLINLNNKIRSIVPGCYNYAVHPDELRILVHYQPSY
YHFNIHIVNIKHPGLGNSIAAGKAILLEDIIEMLNYLGPEGYMNKTITYA
IGENHDLWKRGLEEELTKQLERDGIPKIPKIV
Ligand information
Ligand IDU
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain6trq Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6trq Molecular basis of the selective processing of short mRNA substrates by the DcpS mRNA decapping enzyme.
Resolution2.944 Å
Binding residue
(original residue number in PDB)		F132 G280 N281
Binding residue
(residue number reindexed from 1)		F120 G266 N267
Annotation score2
Enzymatic activity
Enzyme Commision number 3.6.1.59: 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase.
Gene Ontology
Molecular Function
GO:0000340 RNA 7-methylguanosine cap binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044692 exoribonuclease activator activity
GO:0046982 protein heterodimerization activity
GO:0140932 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
Biological Process
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006970 response to osmotic stress
GO:0006979 response to oxidative stress
GO:0007584 response to nutrient
GO:0009267 cellular response to starvation
GO:0009408 response to heat
GO:0031086 nuclear-transcribed mRNA catabolic process, deadenylation-independent decay
GO:0110156 mRNA methylguanosine-cap decapping
Cellular Component
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0048471 perinuclear region of cytoplasm
GO:0106095 m7G(5')pppN diphosphatase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6trq, PDBe:6trq, PDBj:6trq
PDBsum6trq
PubMed32723815
UniProtQ06151|DCPS_YEAST m7GpppX diphosphatase (Gene Name=DCS1)

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