SMTL ID : 9g6t.1

p53-Y220C Core Domain Covalently Bound to 5-Chloro-6-methylpyrazine-2-carbonitrile Soaked at 5 mM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

5 x 01: 5-chloranyl-6-methyl-pyrazine-2-carbonitrile

01.1: 9 residues within 4Å: Chain A: L.52, V.54, T.57, P.58, C.127, E.128, P.129, P.130 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.52 Water bridges: A:T.137 01.2: 3 residues within 4Å: Chain A: K.27, A.183, C.184 No protein-ligand interaction detected (PLIP) 01.13: 8 residues within 4Å: Chain B: L.52, V.54, T.57, P.58, C.127, E.128, P.129, P.130 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.52 Water bridges: B:T.137 01.14: 3 residues within 4Å: Chain B: K.27, A.183, C.184 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.186 01.16: 5 residues within 4Å: Chain A: Q.74 Chain B: H.85, C.89, S.90 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.90

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

EDO.3: 6 residues within 4Å: Chain A: F.20, L.21, S.23, C.31, L.40, P.49 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.21, A:S.23, A:S.23, A:P.49 Water bridges: A:S.23, A:C.31 EDO.5: 6 residues within 4Å: Chain A: R.17, W.53, V.54, D.55, D.135 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:D.135 Water bridges: A:V.54 EDO.7: 5 residues within 4Å: Chain A: S.73, Q.74 Chain B: H.86, D.91 Ligands: 01.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.73 EDO.9: 5 residues within 4Å: Chain A: K.39, R.155, P.157, R.180, E.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.39, A:R.155, A:R.180, A:E.192 EDO.10: 3 residues within 4Å: Chain A: R.180, D.188, E.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.192 EDO.17: 4 residues within 4Å: Chain B: R.17, W.53, V.54, D.55 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.17, B:R.17, B:D.135 Water bridges: B:V.54, B:D.55, B:D.55

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

EPE.4: 5 residues within 4Å: Chain A: K.8, Y.10, L.171, R.174 Chain B: L.108 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.174 EPE.11: 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 EPE.18: 4 residues within 4Å: Chain B: Y.146, S.148, C.182, A.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.148, B:A.183 Water bridges: B:C.184

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

PEG.6: 2 residues within 4Å: Chain A: H.22, G.24 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.22, A:S.23, A:R.189, A:R.189 PEG.15: 2 residues within 4Å: Chain B: H.22, G.24 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.22, B:R.189, B:R.189 PEG.20: 5 residues within 4Å: Chain B: S.13, Y.14, S.56, T.57 Ligands: GOL.21 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.56, B:T.57, B:T.57 Water bridges: B:T.57

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: V.54, D.55, S.56, T.57 Ligands: 01.1, EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.55, A:T.57 Water bridges: A:V.54, A:V.54 GOL.19: 3 residues within 4Å: Chain B: T.9, D.175, S.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.9, B:D.175 GOL.21: 6 residues within 4Å: Chain B: Y.14, T.57, P.58, P.59, P.60 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.14

2 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 ZN.22: 4 residues within 4Å: Chain B: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:H.86, B:C.145, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cellular tumor antigen p53

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