SMTL ID : 9g6u.2 (1 other biounit)

p53-Y220C Core Domain Covalently Bound to 3,5-Dichloro-6-Ethylpyrazine-2-carbonitirle Soaked at 5 mM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

3 x 01: 3,5-bis(chloranyl)-6-ethyl-pyrazine-2-carbonitrile

01.1: 8 residues within 4Å: Chain A: V.54, T.57, P.58, P.59, C.127, E.128, P.129, T.137 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.54 01.2: 3 residues within 4Å: Chain A: H.85, C.89 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) 01.9: 3 residues within 4Å: Chain A: K.27, A.183, C.184 No protein-ligand interaction detected (PLIP)

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

PEG.3: 2 residues within 4Å: Chain A: E.111, Y.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.63, A:R.63 Water bridges: A:E.111, A:D.114

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: T.9, N.38, D.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.9, A:D.175 Water bridges: A:Q.7, A:N.38, A:S.176 GOL.7: 3 residues within 4Å: Chain A: P.97, Q.99, D.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.99, A:D.114 GOL.11: 2 residues within 4Å: Chain A: S.168, N.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.168, A:S.168

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

EDO.5: 2 residues within 4Å: Chain A: H.86 Ligands: 01.2 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: K.46, T.47, E.105 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.47, A:T.47, A:E.105 EDO.12: 3 residues within 4Å: Chain A: E.105, N.142 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.142, A:N.142

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: H.22, S.23, G.24, T.32, R.189 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.24, A:T.32, A:R.189, A:R.189 Water bridges: A:Y.33

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

EPE.8: 5 residues within 4Å: Chain A: Y.146, S.148, R.155, C.182, A.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.148, A:R.155, A:A.183 Water bridges: A:S.148, A:C.184

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 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., SNAr Reactive Pyrazine Derivatives as p53-Y220C Cleft Binders with Diverse Binding Modes. Drug Des Devel Ther (2025)

Release Date

2025-06-11

Peptides

Cellular tumor antigen p53: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cellular tumor antigen p53

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