SMTL ID : 8gcy.1

Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.337, C.340, C.357, C.360 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.337, A:C.340, A:C.357, A:C.360 ZN.2: 4 residues within 4Å: Chain A: C.352, H.354, C.372, C.375 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.352, A:H.354, A:C.372, A:C.375

1 x Z3N: 2-{3-[(1s,3R)-3-methyl-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(3S)-3-methylpiperidin-1-yl]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one(Non-covalent)

Z3N.3: 18 residues within 4Å: Chain A: P.35, P.36, R.105, T.108, K.109, L.112, S.182, T.183, L.186, Y.224, A.226, F.227, T.229, E.232, L.251, Y.327, M.330, G.331 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.108, A:L.112, A:T.183, A:L.186, A:F.227, A:T.229 Hydrogen bonds: A:F.227 Salt bridges: A:E.232 pi-Stacking: A:Y.327

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: N.68, E.69, Y.70, F.130, K.153, T.154, I.155 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.68, A:E.69, A:Y.70, A:T.154, A:I.155 Water bridges: A:T.154, A:T.154

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 7 residues within 4Å: Chain A: L.228, T.229, Y.230, R.250, S.252, T.254, R.255 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.230, A:S.252, A:S.252 Water bridges: A:C.253 Salt bridges: A:R.250, A:R.255

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.6: 6 residues within 4Å: Chain A: R.202, L.203, Q.205, W.259, P.279, L.280 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimani, S.W. et al., The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition. Commun Biol (2023)

Release Date

2023-03-22

Peptides

E3 ubiquitin-protein ligase CBL-B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase CBL-B