Structure of PDB 8u17 Chain D Binding Site BS02

Receptor Information

>8u17 Chain D (length=349) Species: 9606 (Homo sapiens)

TLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTF
AVLAYSQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRT
QSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPSYKWWQKYQK
RKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPID
FSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQET
EITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHS
WFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPD

Ligand information

• Ligand ID: Y70
• InChI: InChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)/t8-/m0/s1
• InChIKey: UVSMNLNDYGZFPF-QMMMGPOBSA-N
• SMILES:
  ACDLabs 12.01: O=C1NC(=O)CCC1N3C(=O)c2cccc(c2C3=O)N
  CACTVS 3.385: Nc1cccc2C(=O)N([C@H]3CCC(=O)NC3=O)C(=O)c12
  OpenEye OEToolkits 1.9.2: c1cc2c(c(c1)N)C(=O)N(C2=O)[C@H]3CCC(=O)NC3=O
  CACTVS 3.385: Nc1cccc2C(=O)N([CH]3CCC(=O)NC3=O)C(=O)c12
  OpenEye OEToolkits 1.9.2: c1cc2c(c(c1)N)C(=O)N(C2=O)C3CCC(=O)NC3=O
• Formula: C13 H11 N3 O4
• Name: S-Pomalidomide
• ChEMBL: CHEMBL2093113
• ZINC: ZINC000003940470
• PDB chain: 8u17 Chain D Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8u17 Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): N351 P352 H353 H378 W380 W386 W400
• Binding residue (residue number reindexed from 1): N272 P273 H274 H299 W301 W307 W321
• Annotation score: 1

External links

• PDB: RCSB:8u17, PDBe:8u17, PDBj:8u17
• PDBsum: 8u17
• PubMed: 38086859
• UniProt: Q96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)