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Structure of PDB 5dv2 Chain A Binding Site BS01

Receptor Information
>5dv2 Chain A (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPPRPWITLKERDSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKK
GIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIM
SEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMT
KDNIGVAVVLEVHKELFKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVK
NILEKASIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKELRYNECLM
NFSRITHGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLG
PLDPQWLVENNITGCPHPHIPSDHFSLLTQLELHP
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain5dv2 Chain A Residue 601 [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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PDB5dv2 Structural basis for inhibition of the deadenylase activity of human CNOT6L
Resolution2.07 Å
Binding residue
(original residue number in PDB)		H360 P365 D410 N412 N480 F485 H530
Binding residue
(residue number reindexed from 1)		H177 P182 D215 N217 N274 F279 H324
Annotation score4
Binding affinityMOAD: ic50=1250uM
PDBbind-CN: -logKd/Ki=2.90,IC50=1250uM
Enzymatic activity
Enzyme Commision number 3.1.13.4: poly(A)-specific ribonuclease.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004535 poly(A)-specific ribonuclease activity

View graph for
Molecular Function
External links
PDB RCSB:5dv2, PDBe:5dv2, PDBj:5dv2
PDBsum5dv2
PubMed27013054
UniProtQ96LI5|CNO6L_HUMAN CCR4-NOT transcription complex subunit 6-like (Gene Name=CNOT6L)

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