SMTL ID : 9g5h.1 (1 other biounit)

p53-Y220C Core Domain Covalently Bound to 2-chloro-5-cyanopyrazine Soaked at 5 mM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

2 x 01: 5-chloranylpyrazine-2-carbonitrile

01.1: 8 residues within 4Å: Chain A: T.57, P.58, P.59, P.60, T.62, C.127, E.128, P.129 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.127 01.2: 3 residues within 4Å: Chain A: K.27, A.183, C.184 No protein-ligand interaction detected (PLIP)

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

EPE.3: 4 residues within 4Å: Chain A: Y.146, S.148, C.182, A.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.148, A:A.183 Water bridges: A:C.184 EPE.8: 4 residues within 4Å: Chain A: K.8, Y.10, L.171, R.174 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.174

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

PEG.4: 2 residues within 4Å: Chain A: H.22, G.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.22 Water bridges: A:S.23, A:R.189, A:R.189

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

EDO.5: 3 residues within 4Å: Chain A: R.17, V.54, D.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:D.55, A:D.55 Water bridges: A:V.54 EDO.6: 3 residues within 4Å: Chain A: G.106, N.107, R.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.106 Water bridges: A:N.107, A:L.108, A:L.108 EDO.7: 3 residues within 4Å: Chain A: R.180, D.188, E.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.188, A:E.192 EDO.9: 3 residues within 4Å: Chain A: S.6, Q.7, K.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.7, A:K.8 Water bridges: A:Q.7, A:T.9 EDO.10: 4 residues within 4Å: Chain A: L.37, N.38, L.159, E.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.38, A:E.178 EDO.11: 5 residues within 4Å: Chain A: K.39, R.155, P.157, R.180, E.192 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.39, A:R.155, A:R.180, A:E.192 Water bridges: A:E.178

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., 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
A

Cellular tumor antigen p53

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