SMTL ID : 8dc7.1

Crystal structure of p53 Y220C covalently bound to indole KG10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Y.13, Q.14, G.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.14, A:G.15 SO4.2: 5 residues within 4Å: Chain A: Y.149, S.151, R.183, S.185, A.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.151, A:R.183, A:A.186 SO4.3: 2 residues within 4Å: Chain A: R.158, R.183 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.183, A:R.183 Salt bridges: A:R.158, A:R.183

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.86, H.89, C.148, C.152 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.86, A:H.89, A:C.148, A:C.152

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 2 residues within 4Å: Chain A: Y.36, N.41 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x R4R: 4-[4-(4-methylpiperazin-1-yl)phenyl]-1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form(Covalent)

R4R.7: 12 residues within 4Å: Chain A: L.55, W.56, V.57, T.60, P.61, C.130, E.131, P.132, P.133, D.138, S.139, T.140 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.55, A:V.57, A:V.57, A:T.60, A:P.132, A:P.133 Hydrogen bonds: A:V.57, A:T.140 Salt bridges: A:D.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guiley, K.Z. et al., A Small Molecule Reacts with the p53 Somatic Mutant Y220C to Rescue Wild-type Thermal Stability. Cancer Discov (2023)

Release Date

2022-10-12

Peptides

Cellular tumor antigen p53: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cellular tumor antigen p53

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