SMTL ID : 8vw5.1 (1 other biounit)

Crystal structure of Cbl-b TKB bound to compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.47, Q.50 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.47, H2O.6

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.188, T.190, N.192, Y.194, E.199 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.188, A:Y.194, A:E.199, A:E.199, H2O.5

1 x 01: [5-(2-{(2R,5S)-2-[2-(carboxymethoxy)-3-methoxy-5-nitrophenyl]-3,5-dimethyl-4-oxoimidazolidin-1-yl}-2-oxoethyl)-3,6-dimethoxy-9,9-dimethyl-9H-xanthen-4-yl]acetic acid

01.3: 12 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, H.279 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.233, A:Y.233, A:Y.233, A:Q.261, A:I.277 Hydrogen bonds: A:S.255, A:S.255 Water bridges: A:R.253 Salt bridges: A:R.253, A:R.258 pi-Cation interactions: A:R.258

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