SMTL ID : 7b47.1

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.8: 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.10: 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 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 QN8.3: 5 residues within 4Å: Chain A: N.146, S.148, V.181, C.182, A.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.148, A:A.183 Water bridges: A:N.146 QN8.6: 6 residues within 4Å: Chain B: Q.51, W.53, S.134, D.135, C.136 Ligands: QNN.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.53 Hydrogen bonds: B:D.135 QN8.11: 4 residues within 4Å: Chain D: Q.51, S.134, D.135, C.136 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.135 QN8.12: 6 residues within 4Å: Chain C: S.13, Y.14 Chain D: S.148, C.182, A.183 Ligands: QNN.13 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.14 Hydrogen bonds: D:S.148, D:A.183 QN8.14: 6 residues within 4Å: Chain C: T.57 Chain D: K.27, V.29, A.183, C.184, P.185 No protein-ligand interaction detected (PLIP)

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

QNN.5: 2 residues within 4Å: Chain B: C.89, P.98 No protein-ligand interaction detected (PLIP) QNN.7: 5 residues within 4Å: Chain B: Q.51, S.134, D.135, C.136 Ligands: QN8.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.135 QNN.9: 2 residues within 4Å: Chain C: Q.51, C.136 No protein-ligand interaction detected (PLIP) QNN.13: 7 residues within 4Å: Chain C: S.13, Y.14 Chain D: S.148, V.181, C.182, A.183 Ligands: QN8.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.14, D:S.148

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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