Structure of PDB 4emr Chain A Binding Site BS01

Receptor Information
>4emr Chain A (length=246) Species: 3672 (Momordica balsamina) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLM
HLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSAR
RKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGA
LLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQ
LAQGNNGVFRTPTVLVDSKGNRVQITNVTSNVVTSNIQLLLNTKNI
Ligand information
Ligand IDMGP
InChIInChI=1S/C11H18N5O14P3/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(28-10)2-27-32(23,24)30-33(25,26)29-31(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H6-,12,13,14,19,20,21,22,23,24,25,26)/p+1/t4-,6-,7-,10-/m1/s1
InChIKeyDKVRNHPCAOHRSI-KQYNXXCUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341C[n+]1cn([C@@H]2O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
OpenEye OEToolkits 1.5.0C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2c[n+](c1c2N=C(N)NC1=O)C)C(O)C3O
CACTVS 3.341C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
FormulaC11 H19 N5 O14 P3
Name7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1234303
DrugBankDB02716
ZINCZINC000015601432
PDB chain4emr Chain A Residue 301 [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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PDB4emr First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		Y70 E85 G109 N110 Y111 E160 R163 E189 S193
Binding residue
(residue number reindexed from 1)		Y70 E85 G109 N110 Y111 E160 R163 E189 S193
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.49,Kd=32.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) I71 E160 R163
Catalytic site (residue number reindexed from 1) I71 E160 R163
Enzyme Commision number 3.2.2.22: rRNA N-glycosylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016787 hydrolase activity
GO:0030598 rRNA N-glycosylase activity
GO:0090729 toxin activity
Biological Process
GO:0017148 negative regulation of translation
GO:0035821 modulation of process of another organism

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4emr, PDBe:4emr, PDBj:4emr
PDBsum4emr
PubMed23280611
UniProtD9J2T9

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