SMTL ID : 8j81.1

MDM2 bound with a peptoid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x UAC: (2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(phenylmethyl)amino]propanoyl]-methyl-amino]propanoyl]amino]propanoyl]-methyl-amino]-N-(3,3-dimethylbutyl)-N-[(2S)-1-oxidanylidene-1-piperazin-1-yl-propan-2-yl]propanamide

UAC.1: 13 residues within 4Å: Chain A: L.43, L.46, G.47, I.50, Y.56, Q.61, V.64, F.75, V.82, H.85, I.88, Y.89 Ligands: CL.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.43, A:L.46, A:I.50, A:I.50, A:Y.56, A:Y.56, A:Q.61, A:V.64, A:V.82, A:I.88, A:Y.89 Hydrogen bonds: A:G.47 Water bridges: A:Q.48

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: E.14, T.15, T.38, M.39, K.40 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: V.97, V.98 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: A.32, Q.33, K.34, Y.37, Y.45 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: K.20, P.21, L.22 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: F.44 Ligands: UAC.1 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.49, K.53, L.70 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.85, R.86 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokomine, M. et al., A structural and physicochemical study of how a peptoid binds to a protein. To Be Published

Release Date

2024-05-01

Peptides

E3 ubiquitin-protein ligase Mdm2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase Mdm2