SMTL ID : 9fqj.2 (1 other biounit)

E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x 01: 2-cyclopropyl-6-methyl-~{N}-[3-[(6~{S})-6-methyl-2-oxidanylidene-1,3-oxazinan-6-yl]phenyl]pyrimidine-4-carboxamide

01.1: 13 residues within 4Å: Chain A: R.108, T.111, K.112, L.115, S.185, T.186, Y.227, A.229, F.230, L.231, Y.330, M.333, G.334 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.108, A:T.111, A:K.112, A:L.231, A:Y.330 Hydrogen bonds: A:F.230, A:Y.330, A:M.333 Water bridges: A:R.108

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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.190, A:N.192, A:Y.194, A:E.199 Water bridges: A:N.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quinn, T.R. et al., Accelerated Discovery of Carbamate Cbl-b Inhibitors Using Generative AI Models and Structure-Based Drug Design. J.Med.Chem. (2024)

Release Date

2024-07-31

Peptides

E3 ubiquitin-protein ligase CBL-B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E3 ubiquitin-protein ligase CBL-B

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