SMTL ID : 7b4e.1

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R282W mutant bound to DNA and MQ: R282W-DNA-MQ

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 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.9: 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

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

QN8.2: 3 residues within 4Å: Chain A: F.20, C.31, P.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.49 QN8.3: 4 residues within 4Å: Chain A: 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, A:C.136 QN8.5: 7 residues within 4Å: Chain A: A.183, C.184 Chain B: C.1, G.2 Chain D: C.9, C.10 Ligands: QNN.4 No protein-ligand interaction detected (PLIP) QN8.10: 3 residues within 4Å: Chain C: F.20, C.31, P.49 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.49 QN8.11: 4 residues within 4Å: Chain C: W.53, S.134, D.135, C.136 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.53 Hydrogen bonds: C:D.135, C:C.136 QN8.13: 7 residues within 4Å: Chain B: C.9, C.10 Chain C: A.183, C.184 Chain D: C.1, G.2 Ligands: QNN.12 No protein-ligand interaction detected (PLIP)

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

QNN.4: 7 residues within 4Å: Chain A: A.183, C.184 Chain B: C.1, G.2 Chain D: C.9, C.10 Ligands: QN8.5 No protein-ligand interaction detected (PLIP) QNN.12: 7 residues within 4Å: Chain B: C.9, C.10 Chain C: A.183, C.184 Chain D: C.1, G.2 Ligands: QN8.13 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 7 residues within 4Å: Chain A: P.84, E.87, R.88 Chain C: P.84, E.87, R.88 Ligands: PG4.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.88 PG4.14: 7 residues within 4Å: Chain A: P.84, E.87, R.88 Chain C: P.84, E.87, R.88 Ligands: PG4.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.88 Water bridges: C:E.87

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

EDO.7: 2 residues within 4Å: Chain A: T.138, H.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.138, A:H.140 Water bridges: A:T.138 EDO.8: 2 residues within 4Å: Chain A: H.86, C.89 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain C: T.138, H.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.140 Water bridges: C:T.138 EDO.16: 2 residues within 4Å: Chain C: H.86, C.89 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: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Cellular tumor antigen p53

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