Structure of PDB 4mx5 Chain X Binding Site BS01

Receptor Information
>4mx5 Chain X (length=263) Species: 3988 (Ricinus communis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPIN
QRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAI
THLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYY
STGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSV
ITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIAL
MVYRCAPPPSSQF
Ligand information
Ligand ID5MX
InChIInChI=1S/C17H17N7O4/c18-16-23-13-12(15(26)24-16)21-8-11(22-13)14(25)19-6-7-20-17(27)28-9-10-4-2-1-3-5-10/h1-5,8H,6-7,9H2,(H,19,25)(H,20,27)(H3,18,22,23,24,26)
InChIKeyFJTRYGAGSOPOQZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)COC(=O)NCCNC(=O)c2cnc3c(n2)N=C(NC3=O)N
CACTVS 3.385NC1=Nc2nc(cnc2C(=O)N1)C(=O)NCCNC(=O)OCc3ccccc3
ACDLabs 12.01O=C(OCc1ccccc1)NCCNC(=O)c2nc3N=C(N)NC(=O)c3nc2
FormulaC17 H17 N7 O4
Namebenzyl (2-{[(2-amino-4-oxo-3,4-dihydropteridin-7-yl)carbonyl]amino}ethyl)carbamate
ChEMBLCHEMBL3098919
DrugBank
ZINCZINC000098208522
PDB chain4mx5 Chain X Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mx5 Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		Y80 V81 G121 N122 Y123 I172 S176 R180
Binding residue
(residue number reindexed from 1)		Y76 V77 G117 N118 Y119 I168 S172 R176
Annotation score1
Binding affinityMOAD: ic50=28uM
PDBbind-CN: -logKd/Ki=4.55,IC50=28uM
BindingDB: IC50=28000nM
Enzymatic activity
Catalytic site (original residue number in PDB) V81
Catalytic site (residue number reindexed from 1) V77
Enzyme Commision number 3.2.2.22: rRNA N-glycosylase.
Gene Ontology
Molecular Function
GO:0030598 rRNA N-glycosylase activity
Biological Process
GO:0017148 negative regulation of translation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4mx5, PDBe:4mx5, PDBj:4mx5
PDBsum4mx5
PubMed24432385
UniProtP02879|RICI_RICCO Ricin

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