› 8qnh

X-ray diffraction
2Å resolution

Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (WO2020264398 Ex23)

Released:
DOI: 10.2210/pdb8qnh/pdb
PDB entry 8qnh coloured by chain, front view.
PDB entry 8qnh coloured by chain, side view.
PDB entry 8qnh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of a Novel Benzodiazepine Series of Cbl-b Inhibitors for the Enhancement of Antitumor Immunity.
Boerth JA, Chinn AJ, Schimpl M, Bommakanti G, Chan C, Code EL, Giblin KA, Gohlke A, Hansel CS, Jin M, Kavanagh SL, Lamb ML, Lane JS, Larner CJB, Mfuh AM, Moore RK, Puri T, Quinn TR, Ye M, Robbins KJ, Gancedo-Rodrigo M, Tang H, Walsh J, Ware J, Wrigley GL, Reddy IK, Zhang Y, Grimster NP
ACS Med Chem Lett 14 1848-1856 (2023)
PMID: 38116444

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171596 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase CBL-B Chain: A
Molecule details ›
Chain: A
Length: 394 amino acids
Theoretical weight: 45.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13191 (Residues: 36-427; Coverage: 40%)
Gene names: CBLB, Nbla00127, RNF56
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand Z3N 1 x Z3N
Ligand ZN 2 x ZN
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 57.04Å b: 73.594Å c: 93.973Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.248
Expression system: Escherichia coli

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