Structure of PDB 5bv3 Chain C Binding Site BS01

Receptor Information
>5bv3 Chain C (length=333) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GMFASLIKRFQFVSVLDSNPQTKVMSLLGTIDNKDAIITAEKTHFLFDET
VRDGRSTPVLYNCENEYSCINGIQELKEITSNDIYYWGLSVIKQDMESNP
TAKLNLIWPATPIHIKKYEQQNFHLVRETPEMYKRIVQPYIEEGRLKWVN
NILYEGAESERVVYKDFSEENKDDGFLILPDMKWDGMNLDSLYLVAIVYR
TDIKTIRDLRYSDRQWLINLNNKIRSIVPGCYNYAVHPDELRILVHYQPS
YYHFNIHIVNIKHPGLGNSIAAGKAILLEDIIEMLNYLGPEGYMNKTITY
AIGENHDLWKRGLEEELTKQLERDGIPKIPKIV
Ligand information
Ligand IDM7G
InChIInChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1
InChIKeySBASPRRECYVBRF-KQYNXXCUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC1OC(n2c[n+](C)c3c2N=C(N)NC3=O)C(O)C1O
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
FormulaC11 H18 N5 O11 P2
Name7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB01960
ZINCZINC000013548083
PDB chain5bv3 Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5bv3 An excess of catalytically required motions inhibits the scavenger decapping enzyme.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		W161 E171 D194 M195 K196 H259 S263 H270
Binding residue
(residue number reindexed from 1)		W148 E158 D181 M182 K183 H246 S250 H257
Annotation score2
Binding affinityMOAD: Kd=68nM
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
View graph for
Cellular Component
External links
PDB RCSB:5bv3, PDBe:5bv3, PDBj:5bv3
PDBsum5bv3
PubMed26258763
UniProtQ06151|DCPS_YEAST m7GpppX diphosphatase (Gene Name=DCS1)

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