SMTL ID : 8rbb.2 (1 other biounit)

p53-Y220C Core Domain Covalently Bound to 2,5,6-trifluoropyridine-3-carbonitrile Soaked at 40 mM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: L.44, D.91 Ligands: YLW.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.91, A:D.91 EDO.6: 7 residues within 4Å: Chain A: T.57, P.58, P.59, P.60, C.127, P.129 Ligands: YLW.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.127 Water bridges: A:C.127 EDO.9: 3 residues within 4Å: Chain A: L.113, D.115, R.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.116

4 x YLW: 2,5-bis(fluoranyl)pyridine-3-carbonitrile(Covalent)

YLW.2: 4 residues within 4Å: Chain A: H.85, H.86, C.89 Ligands: EDO.1 No protein-ligand interaction detected (PLIP) YLW.3: 11 residues within 4Å: Chain A: L.52, V.54, T.57, P.58, C.127, E.128, P.129, P.130, T.137 Ligands: EDO.6, EPE.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.54 YLW.4: 8 residues within 4Å: Chain A: R.17, L.18, G.19, Q.51, L.52, W.53, D.135, C.136 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.53, A:W.53 Hydrogen bonds: A:R.17 Halogen bonds: A:R.17 YLW.5: 3 residues within 4Å: Chain A: K.27, A.183, C.184 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.27

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

EPE.7: 7 residues within 4Å: Chain A: W.53, V.54, D.55, S.56, T.57, D.135 Ligands: YLW.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.57 EPE.8: 4 residues within 4Å: Chain A: Y.146, S.148, C.182, A.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.148, A:S.148, A:A.183 Water bridges: A:S.148, A:C.184

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 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
B

Cellular tumor antigen p53

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