Structure of PDB 8rqc Chain D Binding Site BS03

Receptor Information

>8rqc Chain D (length=312) Species: 9606 (Homo sapiens)

PTSHTYLGADMEEFGRTLHDDDSIQVIPVLPQVMMILVPGQTLPLQLFHP
QEVSMVRNLIQNDRTFAVLAYSNVEREAEFGTTAEIYAYREEQDFGIEIV
KVKAIGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLRE
WDENLKDDSLPSNPIDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELD
IMNKCTSLCCKQCQETEITTKNEIFSLSREGPMAAYVNPHGYVHEILTVY
KACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQK
FWGLTRSALIPT

Ligand information

• Ligand ID: QFC
• InChI: InChI=1S/C32H30FN5O4/c33-26-16-23(17-34)8-9-27(26)37-14-12-36(13-15-37)18-21-4-6-22(7-5-21)20-42-29-3-1-2-24-25(29)19-38(32(24)41)28-10-11-30(39)35-31(28)40/h1-9,16,28H,10-15,18-20H2,(H,35,39,40)/t28-/m0/s1
• InChIKey: YTINZZFBHWSAGL-NDEPHWFRSA-N
• SMILES:
  CACTVS 3.385: Fc1cc(ccc1N2CCN(CC2)Cc3ccc(COc4cccc5C(=O)N(Cc45)[C@H]6CCC(=O)NC6=O)cc3)C#N
  OpenEye OEToolkits 2.0.7: c1cc2c(c(c1)OCc3ccc(cc3)CN4CCN(CC4)c5ccc(cc5F)C#N)CN(C2=O)C6CCC(=O)NC6=O
  ACDLabs 12.01: O=C1NC(=O)CCC1N1Cc2c(cccc2OCc2ccc(cc2)CN2CCN(CC2)c2ccc(C#N)cc2F)C1=O
  CACTVS 3.385: Fc1cc(ccc1N2CCN(CC2)Cc3ccc(COc4cccc5C(=O)N(Cc45)[CH]6CCC(=O)NC6=O)cc3)C#N
  OpenEye OEToolkits 2.0.7: c1cc2c(c(c1)OCc3ccc(cc3)CN4CCN(CC4)c5ccc(cc5F)C#N)CN(C2=O)[C@H]6CCC(=O)NC6=O
• Formula: C32 H30 F N5 O4
• Name: Mezigdomide
• ChEMBL: CHEMBL4648616
• DrugBank: DB17584
• PDB chain: 8rqc Chain D Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rqc Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): F102 F150 I152 N351 P352 H353 E377 H378 S379 W380 W386 W400 F402
• Binding residue (residue number reindexed from 1): F48 F95 I97 N238 P239 H240 E264 H265 S266 W267 W273 W287 F289
• Annotation score: 1

External links

• PDB: RCSB:8rqc, PDBe:8rqc, PDBj:8rqc
• PDBsum: 8rqc
• UniProt: Q96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)