SMTL ID : 7b4n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 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.7: 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

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

QN8.2: 7 residues within 4Å: Chain A: L.21, H.22, S.23, T.30, C.31, T.47, P.49 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.21 Water bridges: A:L.21, A:T.30 QN8.3: 5 residues within 4Å: Chain A: W.53, S.134, D.135, C.136, T.138 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.53 Water bridges: A:D.135 QN8.8: 7 residues within 4Å: Chain C: L.21, H.22, S.23, T.30, C.31, T.47, P.49 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.21 Water bridges: C:L.21 QN8.9: 5 residues within 4Å: Chain C: W.53, S.134, D.135, C.136, T.138 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.53 Water bridges: C:D.135, C:T.138

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

QNN.4: 6 residues within 4Å: Chain A: K.27, A.183, C.184 Chain B: G.2 Chain D: C.9, C.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.27 QNN.10: 6 residues within 4Å: Chain B: C.9, C.10 Chain C: K.27, A.183, C.184 Chain D: G.2 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.27

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 3 residues within 4Å: Chain A: N.154, R.155, R.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.154 Water bridges: A:N.154 FMT.6: 7 residues within 4Å: Chain A: L.18, F.20, Y.33, N.38, N.175, S.176, F.177 No protein-ligand interaction detected (PLIP) FMT.11: 3 residues within 4Å: Chain C: N.154, R.155, R.156 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.154 Water bridges: C:N.154 FMT.12: 7 residues within 4Å: Chain C: L.18, F.20, Y.33, N.38, N.175, S.176, F.177 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.33

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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