Structure of PDB 8rq9 Chain C Binding Site BS01

Receptor Information
>8rq9 Chain C (length=312) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTL
PLQLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREE
QDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPEAETLMDRIKK
QLREWDEDSLPSNPIDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELD
IMNKCTSLCCKQCQETEITTKNEIFSLSREGPMAAYVNPHGYVHEILTVY
KACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQK
FWGLTRSALIPT
Ligand information
Ligand IDA1H2F
InChIInChI=1S/C47H50ClN9O3/c1-30-52-53-46-47(20-21-47)51-43(32-10-13-35(48)14-11-32)38-26-33(12-15-40(38)57(30)46)34-27-49-55(28-34)23-6-4-2-3-5-22-54-24-18-31(19-25-54)36-8-7-9-37-39(36)29-56(45(37)60)41-16-17-42(58)50-44(41)59/h7-15,26-28,31,41H,2-6,16-25,29H2,1H3,(H,50,58,59)/t41-/m0/s1
InChIKeySDKKICDYRHTFNX-RWYGWLOXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1nnc2n1c3ccc(cc3C(=NC24CC4)c5ccc(Cl)cc5)c6cnn(CCCCCCCN7CCC(CC7)c8cccc9C(=O)N(Cc89)[CH]%10CCC(=O)NC%10=O)c6
OpenEye OEToolkits 2.0.7Cc1nnc2n1-c3ccc(cc3C(=NC24CC4)c5ccc(cc5)Cl)c6cnn(c6)CCCCCCCN7CCC(CC7)c8cccc9c8CN(C9=O)C1CCC(=O)NC1=O
OpenEye OEToolkits 2.0.7Cc1nnc2n1-c3ccc(cc3C(=NC24CC4)c5ccc(cc5)Cl)c6cnn(c6)CCCCCCCN7CCC(CC7)c8cccc9c8CN(C9=O)[C@H]1CCC(=O)NC1=O
CACTVS 3.385Cc1nnc2n1c3ccc(cc3C(=NC24CC4)c5ccc(Cl)cc5)c6cnn(CCCCCCCN7CCC(CC7)c8cccc9C(=O)N(Cc89)[C@H]%10CCC(=O)NC%10=O)c6
FormulaC47 H50 Cl N9 O3
Name(3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione
ChEMBL
DrugBank
ZINC
PDB chain8rq9 Chain C 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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PDB8rq9 Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders
Resolution2.91 Å
Binding residue
(original residue number in PDB)
P352 H378 W380 W386 W400 F402
Binding residue
(residue number reindexed from 1)
P239 H265 W267 W273 W287 F289
Annotation score1
External links
PDB RCSB:8rq9, PDBe:8rq9, PDBj:8rq9
PDBsum8rq9
PubMed
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

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