Structure of PDB 5ulj Chain B Binding Site BS02

Receptor Information
>5ulj Chain B (length=386) Species: 322104 (Scheffersomyces stipitis CBS 6054) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPRGSHMMKTLSLQSRAKKQPKEIFAFARDIDGEFVYDQKIVKDENVSY
YYLPDSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNG
EKVNVDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELA
RRKEEDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWAKKMVNNYE
QYISVIKTGIGEAKMLLAGEVDCVWDYIPEDGKDVLSHYMELKTTRILES
NGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIPL
LIKNNALTENKSGGKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFD
PSTRTFTLRELMGNENSRLRNGEMLTSEFKQWRESI
Ligand information
Ligand ID0WD
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-15(31)16(44-46(33,34)35)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)14(30)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyONOVTRNLNDQWGA-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O[P](O)(O)=O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)OP(=O)(O)O)O)N
CACTVS 3.370NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O[P](O)(O)=O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)OP(=O)(O)O)O)N
FormulaC21 H30 N7 O17 P3
Name
ChEMBL
DrugBank
ZINCZINC000085629102
PDB chain5ulj Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ulj 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
Resolution1.911 Å
Binding residue
(original residue number in PDB)		N76 M77 Y107 R108 G109 S140 E145 Y176 Q209 G227 E228 K251
Binding residue
(residue number reindexed from 1)		N79 M80 Y110 R111 G112 S143 E148 Y179 Q201 G219 E220 K243
Annotation score2
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0034353 mRNA 5'-diphosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006397 mRNA processing
GO:0110155 NAD-cap decapping
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ulj, PDBe:5ulj, PDBj:5ulj
PDBsum5ulj
PubMed28283058
UniProtA3LNL5|DXO_PICST Decapping nuclease RAI1 (Gene Name=RAI1)

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