Structure of PDB 8rq9 Chain A Binding Site BS01

Receptor Information
>8rq9 Chain A (length=316) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVP
GQTLPLQLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYA
YREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPEAETLMD
RIKKQLREWDEDSLPSNPIDFSYWVAANLPIDDSLRIQLLKIDSAIQRLR
CELDIMNKCTSLCCKQCQETEITTKNEIFSLSREGPMAAYVNPHGYVHEI
LTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDM
SPQKFWGLTRSALIPT
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 A 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)
H378 W380 W386 F402
Binding residue
(residue number reindexed from 1)
H269 W271 W277 F293
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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