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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

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

YLW.1: 10 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.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.54, A:P.58, A:T.137

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

PEG.2: 2 residues within 4Å: Chain A: H.22, G.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.22 Water bridges: A:R.189, A:R.189 PEG.3: 5 residues within 4Å: Chain A: T.9, N.38, D.175, S.176 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.11

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

EDO.4: 5 residues within 4Å: Chain A: L.37, N.38, K.71, E.178 Ligands: PEG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.38, A:K.71 Water bridges: A:S.176 EDO.5: 7 residues within 4Å: Chain A: V.54, D.55, S.56, T.57, P.130 Ligands: YLW.1, EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.55 Water bridges: A:V.54, A:T.57, A:D.135 EDO.6: 6 residues within 4Å: Chain A: R.17, W.53, V.54, D.55, D.135 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:D.55, A:D.55, A:D.135 Water bridges: A:V.54 EDO.8: 6 residues within 4Å: Chain A: L.21, H.22, S.23, C.31, T.32, Y.33 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:T.32, A:Y.33 Water bridges: A:R.189, A:R.189 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 EDO.10: 3 residues within 4Å: Chain A: L.44, H.86, D.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:D.91 Water bridges: A:H.86, A:H.86 EDO.11: 2 residues within 4Å: Chain A: S.168, N.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.168, A:N.170, A:N.170

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

EPE.7: 4 residues within 4Å: Chain A: Y.146, S.148, C.182, A.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.148, A:A.183 Water bridges: A:S.148, A:C.184

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 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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