SMTL ID : 8qni.1

Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (benzodiazepine compound 25)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

monomer

Ligands

1 x W7R: 2-[[(2~{S})-2-methylmorpholin-4-yl]methyl]-~{N}-[(3~{S})-2-oxidanylidene-5-phenyl-1,3-dihydropyrido[3,4-e][1,4]diazepin-3-yl]benzamide(Non-covalent)

W7R.1: 16 residues within 4Å: Chain A: K.112, L.115, I.116, H.119, S.185, T.186, L.189, Y.227, M.228, A.229, F.230, L.231, L.254, Y.330, M.333, G.334 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.112, A:L.115, A:I.116, A:L.189, A:A.229, A:F.230, A:L.254, A:Y.330, A:Y.330, A:M.333 Hydrogen bonds: A:F.230, A:F.230 pi-Stacking: A:Y.227

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.340, C.343, C.360, C.363 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.340, A:C.343, A:C.360, A:C.363 ZN.3: 4 residues within 4Å: Chain A: C.355, H.357, C.375, C.378 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.355, A:H.357, A:C.375, A:C.378

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: D.188, T.190, N.192, Y.194, E.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.190, A:E.199 Water bridges: A:N.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boerth, J.A. et al., Discovery of a Novel Benzodiazepine Series of Cbl-b Inhibitors for the Enhancement of Antitumor Immunity. Acs Med.Chem.Lett. (2023)

Release Date

2023-11-22

Peptides

E3 ubiquitin-protein ligase CBL-B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase CBL-B

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