SMTL ID : 7b4b.1

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C mutant bound to MQ: R273C-MQ (I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.6: 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 ZN.11: 4 residues within 4Å: Chain C: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.83, C:H.86, C:C.145, C:C.149 ZN.19: 4 residues within 4Å: Chain D: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.83, D:H.86, D:C.145, D:C.149

4 x QN8: (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)

QN8.2: 5 residues within 4Å: Chain A: Q.51, W.53, S.134, D.135, C.136 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.53 Hydrogen bonds: A:D.135 Water bridges: A:S.134 QN8.8: 5 residues within 4Å: Chain B: Q.51, W.53, S.134, D.135, C.136 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.53 Hydrogen bonds: B:D.135 Water bridges: B:S.134 QN8.9: 6 residues within 4Å: Chain B: K.39, S.147, R.155, P.157, C.180, E.192 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.157 Hydrogen bonds: B:K.39, B:S.147 Salt bridges: B:E.192 QN8.14: 4 residues within 4Å: Chain C: C.182, R.187, D.188 Ligands: QNN.13 3 PLIP interactions: 3 interactions with chain C Water bridges: C:A.183, C:D.188 Salt bridges: C:D.188

6 x QNN: (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)

QNN.3: 6 residues within 4Å: Chain A: K.39, S.147, R.155, P.157, C.180, E.192 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.157 Hydrogen bonds: A:K.39 Salt bridges: A:E.192 QNN.7: 2 residues within 4Å: Chain B: C.89, P.98 No protein-ligand interaction detected (PLIP) QNN.10: 4 residues within 4Å: Chain B: K.27, Q.43, A.183, C.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.43 QNN.12: 3 residues within 4Å: Chain C: Q.51, W.53, C.136 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.53 Water bridges: C:T.138 QNN.13: 7 residues within 4Å: Chain C: K.39, S.147, R.155, P.157, C.180, E.192 Ligands: QN8.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.39 Salt bridges: C:E.192 QNN.20: 6 residues within 4Å: Chain D: K.39, S.147, R.155, P.157, C.180, E.192 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.157 Hydrogen bonds: D:K.39 Salt bridges: D:E.192

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

EDO.4: 3 residues within 4Å: Chain A: K.71, Q.72, P.157 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.73 EDO.5: 7 residues within 4Å: Chain A: P.60, G.61, T.62, R.109, P.126, Y.127, E.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.61, A:T.62, A:R.109, A:R.109 EDO.15: 5 residues within 4Å: Chain B: R.190 Chain C: G.61, R.63, P.126, S.167 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.190 Water bridges: C:Y.127 EDO.16: 5 residues within 4Å: Chain C: Q.74, H.75, M.76, T.77, E.78 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.75, C:T.77, C:E.78

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

PEG.17: 5 residues within 4Å: Chain C: V.4, P.5, S.6, Q.7, K.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.4, C:Q.7, C:K.8 PEG.18: 2 residues within 4Å: Chain C: E.193, N.195 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Degtjarik, O. et al., Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Nat Commun (2021)

Release Date

2021-12-08

Peptides

Cellular tumor antigen p53: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cellular tumor antigen p53

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