SMTL ID : 9fqi.1

E3 ligase Cbl-b in complex with a lactam scaffold inhibitor (compound 7)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x 01: 8-[3-[(4~{R})-4-methyl-2-oxidanylidene-piperidin-4-yl]phenyl]-3-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one

01.1: 16 residues within 4Å: Chain A: P.38, P.39, R.108, T.111, K.112, L.115, S.185, T.186, L.189, Y.227, A.229, F.230, E.235, Y.330, M.333, G.334 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.111, A:L.189, A:Y.330 Hydrogen bonds: A:F.230, A:Y.330, A:M.333 Salt bridges: A:E.235

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:T.190 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
A

E3 ubiquitin-protein ligase CBL-B

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