SMTL ID : 7bj6.1

Inhibitor of MDM2-p53 Interaction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 4 residues within 4Å: Chain A: A.59, Q.60, Q.61, H.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.61, A:H.62

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

EDO.2: 5 residues within 4Å: Chain A: Y.49, K.53, D.69, L.70 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.49, A:K.53, A:D.69, A:L.70 EDO.3: 5 residues within 4Å: Chain A: S.29, Y.49, K.53, L.70 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.29, A:S.29, A:K.53

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

SO4.4: 3 residues within 4Å: Chain A: K.34, D.35, T.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.35, A:T.36 SO4.5: 1 residues within 4Å: Chain A: R.86 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.86 SO4.6: 3 residues within 4Å: Chain A: L.16, V.17, R.18 No protein-ligand interaction detected (PLIP)

1 x TVK: (3~{R})-2-[(5-chloranylpyridin-2-yl)methyl]-3-(4-chlorophenyl)-4-fluoranyl-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-6-(2-oxidanylpropan-2-yl)isoindol-1-one(Non-covalent)

TVK.7: 18 residues within 4Å: Chain A: L.43, F.44, L.46, G.47, Q.48, I.50, M.51, Y.56, Q.61, H.62, I.63, V.64, F.75, F.80, V.82, H.85, I.88, Y.89 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.43, A:L.46, A:I.50, A:I.50, A:V.82 Hydrogen bonds: A:Q.61 Halogen bonds: A:G.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chessari, G. et al., Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein-Protein Interaction. J.Med.Chem. (2021)

Release Date

2021-04-07

Peptides

E3 ubiquitin-protein ligase Mdm2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase Mdm2

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