SMTL ID : 7b4d.1

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 QNN: (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)(Non-covalent)

QNN.2: 6 residues within 4Å: Chain A: L.21, S.23, V.29, T.30, C.31 Ligands: FMT.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.21 QNN.4: 5 residues within 4Å: Chain A: Q.51, W.53, S.134, C.136 Ligands: QN8.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.53 Hydrogen bonds: A:S.134 QNN.5: 7 residues within 4Å: Chain A: K.27, S.28, Q.43, A.183, C.184 Chain B: C.9 Chain D: G.2 No protein-ligand interaction detected (PLIP) QNN.10: 6 residues within 4Å: Chain C: L.21, S.23, V.29, T.30, C.31 Ligands: FMT.14 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.21 QNN.12: 5 residues within 4Å: Chain C: Q.51, W.53, S.134, C.136 Ligands: QN8.11 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.53 Hydrogen bonds: C:S.134 QNN.13: 7 residues within 4Å: Chain B: G.2 Chain C: K.27, S.28, Q.43, A.183, C.184 Chain D: C.9 No protein-ligand interaction detected (PLIP)

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

QN8.3: 5 residues within 4Å: Chain A: Q.51, W.53, S.134, C.136 Ligands: QNN.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.53 Water bridges: A:Q.51 QN8.11: 5 residues within 4Å: Chain C: Q.51, W.53, S.134, C.136 Ligands: QNN.12 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.53 Water bridges: C:Q.51

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

FMT.6: 1 residues within 4Å: Ligands: QNN.2 No protein-ligand interaction detected (PLIP) FMT.7: 1 residues within 4Å: Chain A: S.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.168, A:S.168 FMT.8: 1 residues within 4Å: Chain A: Q.74 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.77 FMT.14: 1 residues within 4Å: Ligands: QNN.10 No protein-ligand interaction detected (PLIP) FMT.15: 1 residues within 4Å: Chain C: S.168 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.168, C:S.168 FMT.16: 1 residues within 4Å: Chain C: Q.74 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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