SMTL ID : 8rbc.1 (1 other biounit)

p53-Y220C Core Domain Covalently Bound to 3-amino-5-chloropyrazine-2,6-dicarbonitrile Soaked at 5 mM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

2 x YM0: 3-azanylpyrazine-2,6-dicarbonitrile(Covalent)

YM0.1: 9 residues within 4Å: Chain A: L.52, V.54, T.57, P.58, C.127, E.128, P.129, P.130, T.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.127 YM0.2: 3 residues within 4Å: Chain A: H.85, H.86, C.89 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain A: Y.146, S.148, R.155, R.180, C.182, A.183, D.188 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.148, A:R.155, A:A.183, A:D.188 Salt bridges: A:R.180 pi-Cation interactions: A:Y.146

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: L.21, S.23, C.31, Y.33, P.49 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.49 Hydrogen bonds: A:L.21, A:Y.33 Water bridges: A:L.21

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:H.86, A:C.145, A:C.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klett, T. et al., Covalent Fragments Acting as Tyrosine Mimics for Mutant p53-Y220C Rescue by Nucleophilic Aromatic Substitution. Acs Pharmacol Transl Sci (2024)

Release Date

2024-11-27

Peptides

Cellular tumor antigen p53: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cellular tumor antigen p53

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