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BioLiP

Structure of PDB 5yj0 Chain S Binding Site BS01

Receptor Information
>5yj0 Chain S (length=93) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPTSLCCKQCQETEITTKNEIFSLSHETLTVYKASNLNLIGRPSTVHSWF
PGYAWTIAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLP
Ligand information
Ligand IDEF2
InChIInChI=1S/C13H10N2O4/c16-10-6-5-9(11(17)14-10)15-12(18)7-3-1-2-4-8(7)13(15)19/h1-4,9H,5-6H2,(H,14,16,17)/t9-/m0/s1
InChIKeyUEJJHQNACJXSKW-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc2c(c1)C(=O)N(C2=O)[C@H]3CCC(=O)NC3=O
CACTVS 3.385O=C1CC[CH](N2C(=O)c3ccccc3C2=O)C(=O)N1
OpenEye OEToolkits 1.9.2c1ccc2c(c1)C(=O)N(C2=O)C3CCC(=O)NC3=O
CACTVS 3.385O=C1CC[C@H](N2C(=O)c3ccccc3C2=O)C(=O)N1
ACDLabs 12.01O=C1NC(=O)CCC1N3C(=O)c2ccccc2C3=O
FormulaC13 H10 N2 O4
NameS-Thalidomide
ChEMBLCHEMBL426123
DrugBank
ZINCZINC000001530947
PDB chain5yj0 Chain S Residue 501 [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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PDB5yj0 Structural basis of thalidomide enantiomer binding to cereblon
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H381 S382 W383 W389 W403 F405
Binding residue
(residue number reindexed from 1)		H47 S48 W49 W55 W69 F71
Annotation score1
Binding affinityMOAD: Kd=5.7uM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5yj0, PDBe:5yj0, PDBj:5yj0
PDBsum5yj0
PubMed29358579
UniProtQ8C7D2|CRBN_MOUSE Protein cereblon (Gene Name=Crbn)

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