SMTL ID : 8vw4.1 (1 other biounit)

Crystal structure of Cbl-b TKB bound to compound 26

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.188, T.190, N.192, Y.194, E.199 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.188, A:T.190, A:Y.194, A:E.199, A:E.199

1 x 01: (7-methoxy-2-{2-[(1S,3S,4S)-3-(3-methoxy-2-methyl-5-nitrophenyl)-1-methyl-5-oxo-1,5-dihydroimidazo[1,5-a]pyridin-2(3H)-yl]-2-oxoethoxy}quinolin-8-yl)acetic acid

01.2: 11 residues within 4Å: Chain A: Y.233, R.253, L.254, S.255, R.258, Q.261, W.262, A.263, Q.275, T.276, I.277 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.233, A:Q.261, A:I.277, A:I.277, A:I.277 Hydrogen bonds: A:S.255 Water bridges: A:Y.233, A:R.253 Salt bridges: A:R.253, A:R.258 pi-Stacking: A:Y.233

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: Y.227, M.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.227 GOL.4: 5 residues within 4Å: Chain A: T.111, L.115, F.230, L.231, E.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.230 GOL.5: 6 residues within 4Å: Chain A: S.185, T.186, L.189, Y.227, A.229, F.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.186, A:Y.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, J. et al., Optimization of a Novel DEL Hit That Binds in the Cbl-b SH2 Domain and Blocks Substrate Binding. Acs Med.Chem.Lett. (2024)

Release Date

2024-07-03

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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