Structure of PDB 5ulj Chain A Binding Site BS02

Receptor Information
>5ulj Chain A (length=381) Species: 322104 (Scheffersomyces stipitis CBS 6054) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKTLSLQSRAKTTALKQPKEIFAFARDIDGEFVYDQKIVKDENVSYYYLP
DSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNGEKVN
VDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELARRKE
EDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWADCSRQQIMVNNY
EQYISVIKTGIGEAKMLLAGEVDCVWDYIPEDGKDVLSHYMELKTTRILE
SNGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIP
LLIKNNALGKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFDPSTRT
FTLRELMGNENSRLRNGEMLTSEFKQWRESI
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 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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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 R108 G109 Y176 Q209 G227 E228 K251 Q275
Binding residue
(residue number reindexed from 1)		N75 R107 G108 Y175 Q202 G220 E221 K244 Q268
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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