SMTL ID : 7b4c.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 (II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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.4: 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.10: 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.13: 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

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

QNN.2: 7 residues within 4Å: Chain A: K.39, S.147, R.155, P.157, C.180, E.192 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.39, A:R.155 Salt bridges: A:E.192 QNN.5: 6 residues within 4Å: Chain B: K.39, S.147, R.155, R.156, P.157, C.180 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.157 Hydrogen bonds: B:K.39 Salt bridges: B:E.192 QNN.7: 1 residues within 4Å: Chain B: C.89 No protein-ligand interaction detected (PLIP) QNN.9: 6 residues within 4Å: Chain B: R.17, L.18, G.19, W.53 Chain C: C.89, P.98 No protein-ligand interaction detected (PLIP) QNN.11: 6 residues within 4Å: Chain C: K.39, S.147, R.155, P.157, C.180, E.192 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.39 Salt bridges: C:E.192 QNN.14: 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.3: 8 residues within 4Å: Chain A: N.146, S.147, S.148, R.155, C.180, V.181, C.182 Ligands: QNN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.148, A:S.148, A:R.155 EDO.8: 3 residues within 4Å: Chain B: P.84, E.87, R.88 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.87 Water bridges: A:N.170 EDO.12: 1 residues within 4Å: Chain C: H.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.22 EDO.15: 1 residues within 4Å: Chain D: R.116 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.116

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

QN8.6: 2 residues within 4Å: Chain B: K.27, C.184 No protein-ligand interaction detected (PLIP)

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

PEG.16: 2 residues within 4Å: Chain D: N.117, T.118 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.115 PEG.17: 3 residues within 4Å: Chain D: L.21, H.22, S.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.22, D:H.22

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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