- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.42 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x QN8: (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)
QN8.2: 4 residues within 4Å:- Chain A: Q.51, W.53, S.134, C.136
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:W.53
QN8.18: 4 residues within 4Å:- Chain B: Q.51, W.53, S.134, C.136
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:W.53
QN8.38: 4 residues within 4Å:- Chain D: Q.51, W.53, S.134, C.136
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:W.53
QN8.54: 4 residues within 4Å:- Chain E: Q.51, W.53, S.134, C.136
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:W.53
- 4 x QNN: (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)
QNN.3: 7 residues within 4Å:- Chain A: K.27, S.28, A.183, C.184
- Chain C: G.2
- Chain F: C.19, C.20
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:K.27
QNN.19: 8 residues within 4Å:- Chain B: K.27, S.28, A.183, C.184
- Chain C: C.11, G.12
- Chain F: C.9, C.10
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:K.27
QNN.39: 7 residues within 4Å:- Chain C: C.19, C.20
- Chain D: K.27, S.28, A.183, C.184
- Chain F: G.2
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:K.27
QNN.55: 8 residues within 4Å:- Chain C: C.9, C.10
- Chain E: K.27, S.28, A.183, C.184
- Chain F: C.11, G.12
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:K.27
- 48 x FMT: FORMIC ACID(Non-functional Binders)
FMT.4: 5 residues within 4Å:- Chain A: R.17, L.18, G.19, W.53
- Ligands: ACT.13
Ligand excluded by PLIPFMT.5: 3 residues within 4Å:- Chain A: R.155
- Chain C: G.8, C.9
Ligand excluded by PLIPFMT.6: 2 residues within 4Å:- Chain A: K.71, Q.72
Ligand excluded by PLIPFMT.7: 3 residues within 4Å:- Chain A: Y.112, L.113, D.114
Ligand excluded by PLIPFMT.8: 8 residues within 4Å:- Chain A: L.18, F.20, Y.33, N.38, N.175, S.176, F.177
- Ligands: ACT.13
Ligand excluded by PLIPFMT.9: 8 residues within 4Å:- Chain A: S.73, Q.74, H.75, M.76, T.77
- Chain B: T.47, E.105, H.140
Ligand excluded by PLIPFMT.10: 5 residues within 4Å:- Chain A: R.17, W.53, V.54, D.55, D.135
Ligand excluded by PLIPFMT.11: 4 residues within 4Å:- Chain A: E.128, T.137, T.138, I.139
Ligand excluded by PLIPFMT.12: 5 residues within 4Å:- Chain A: D.93, R.103, V.104, E.105, N.142
Ligand excluded by PLIPFMT.20: 5 residues within 4Å:- Chain B: R.17, L.18, G.19, W.53
- Ligands: ACT.30
Ligand excluded by PLIPFMT.21: 2 residues within 4Å:- Chain B: K.71, Q.72
Ligand excluded by PLIPFMT.22: 8 residues within 4Å:- Chain B: L.18, F.20, Y.33, N.38, N.175, S.176, F.177
- Ligands: ACT.30
Ligand excluded by PLIPFMT.23: 3 residues within 4Å:- Chain B: Y.112, L.113, D.114
Ligand excluded by PLIPFMT.24: 3 residues within 4Å:- Chain B: R.155
- Chain C: G.18, C.19
Ligand excluded by PLIPFMT.25: 5 residues within 4Å:- Chain B: S.73, Q.74, H.75, M.76, T.77
Ligand excluded by PLIPFMT.26: 5 residues within 4Å:- Chain B: H.180, D.188, T.191, E.192
- Chain F: T.7
Ligand excluded by PLIPFMT.27: 5 residues within 4Å:- Chain B: R.17, W.53, V.54, D.55, D.135
Ligand excluded by PLIPFMT.28: 5 residues within 4Å:- Chain B: N.107, E.128, T.137, T.138, I.139
Ligand excluded by PLIPFMT.29: 5 residues within 4Å:- Chain B: D.93, R.103, V.104, E.105, N.142
Ligand excluded by PLIPFMT.32: 3 residues within 4Å:- Chain C: A.6, T.7
- Ligands: FMT.36
Ligand excluded by PLIPFMT.33: 3 residues within 4Å:- Chain C: A.16, T.17
- Chain D: T.191
Ligand excluded by PLIPFMT.34: 5 residues within 4Å:- Chain C: T.17
- Chain D: H.180, D.188, T.191, E.192
Ligand excluded by PLIPFMT.35: 3 residues within 4Å:- Chain C: T.17
- Chain F: G.4, C.5
Ligand excluded by PLIPFMT.36: 4 residues within 4Å:- Chain C: T.7
- Chain F: G.14, C.15
- Ligands: FMT.32
Ligand excluded by PLIPFMT.40: 5 residues within 4Å:- Chain D: R.17, L.18, G.19, W.53
- Ligands: ACT.49
Ligand excluded by PLIPFMT.41: 3 residues within 4Å:- Chain D: R.155
- Chain F: G.8, C.9
Ligand excluded by PLIPFMT.42: 2 residues within 4Å:- Chain D: K.71, Q.72
Ligand excluded by PLIPFMT.43: 3 residues within 4Å:- Chain D: Y.112, L.113, D.114
Ligand excluded by PLIPFMT.44: 8 residues within 4Å:- Chain D: L.18, F.20, Y.33, N.38, N.175, S.176, F.177
- Ligands: ACT.49
Ligand excluded by PLIPFMT.45: 8 residues within 4Å:- Chain D: S.73, Q.74, H.75, M.76, T.77
- Chain E: T.47, E.105, H.140
Ligand excluded by PLIPFMT.46: 5 residues within 4Å:- Chain D: R.17, W.53, V.54, D.55, D.135
Ligand excluded by PLIPFMT.47: 4 residues within 4Å:- Chain D: E.128, T.137, T.138, I.139
Ligand excluded by PLIPFMT.48: 5 residues within 4Å:- Chain D: D.93, R.103, V.104, E.105, N.142
Ligand excluded by PLIPFMT.56: 5 residues within 4Å:- Chain E: R.17, L.18, G.19, W.53
- Ligands: ACT.66
Ligand excluded by PLIPFMT.57: 2 residues within 4Å:- Chain E: K.71, Q.72
Ligand excluded by PLIPFMT.58: 8 residues within 4Å:- Chain E: L.18, F.20, Y.33, N.38, N.175, S.176, F.177
- Ligands: ACT.66
Ligand excluded by PLIPFMT.59: 3 residues within 4Å:- Chain E: Y.112, L.113, D.114
Ligand excluded by PLIPFMT.60: 3 residues within 4Å:- Chain E: R.155
- Chain F: G.18, C.19
Ligand excluded by PLIPFMT.61: 5 residues within 4Å:- Chain E: S.73, Q.74, H.75, M.76, T.77
Ligand excluded by PLIPFMT.62: 5 residues within 4Å:- Chain C: T.7
- Chain E: H.180, D.188, T.191, E.192
Ligand excluded by PLIPFMT.63: 5 residues within 4Å:- Chain E: R.17, W.53, V.54, D.55, D.135
Ligand excluded by PLIPFMT.64: 5 residues within 4Å:- Chain E: N.107, E.128, T.137, T.138, I.139
Ligand excluded by PLIPFMT.65: 5 residues within 4Å:- Chain E: D.93, R.103, V.104, E.105, N.142
Ligand excluded by PLIPFMT.68: 3 residues within 4Å:- Chain F: A.6, T.7
- Ligands: FMT.72
Ligand excluded by PLIPFMT.69: 3 residues within 4Å:- Chain A: T.191
- Chain F: A.16, T.17
Ligand excluded by PLIPFMT.70: 5 residues within 4Å:- Chain A: H.180, D.188, T.191, E.192
- Chain F: T.17
Ligand excluded by PLIPFMT.71: 3 residues within 4Å:- Chain C: G.4, C.5
- Chain F: T.17
Ligand excluded by PLIPFMT.72: 4 residues within 4Å:- Chain C: G.14, C.15
- Chain F: T.7
- Ligands: FMT.68
Ligand excluded by PLIP- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.13: 5 residues within 4Å:- Chain A: L.18, F.20, Y.33
- Ligands: FMT.4, FMT.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.33
- Water bridges: A:L.18, A:L.18
ACT.30: 5 residues within 4Å:- Chain B: L.18, F.20, Y.33
- Ligands: FMT.20, FMT.22
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.33
- Water bridges: B:L.18, B:L.18
ACT.49: 5 residues within 4Å:- Chain D: L.18, F.20, Y.33
- Ligands: FMT.40, FMT.44
2 PLIP interactions:2 interactions with chain D- Water bridges: D:L.18, D:L.18
ACT.66: 5 residues within 4Å:- Chain E: L.18, F.20, Y.33
- Ligands: FMT.56, FMT.58
2 PLIP interactions:2 interactions with chain E- Water bridges: E:L.18, E:L.18
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.14: 2 residues within 4Å:- Chain A: E.131, V.132
1 PLIP interactions:1 interactions with chain A- Water bridges: A:V.132
EDO.15: 5 residues within 4Å:- Chain A: Y.10, L.171, R.174
- Chain B: E.131, V.132
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:R.174, A:R.174
- Water bridges: B:V.132
EDO.16: 6 residues within 4Å:- Chain A: P.129, P.130, E.131, S.134, C.136, T.137
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.131, A:E.131, A:E.131, A:S.134, A:T.137
EDO.31: 6 residues within 4Å:- Chain B: P.129, P.130, E.131, S.134, C.136, T.137
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.128, B:E.131, B:E.131, B:E.131, B:S.134
EDO.50: 2 residues within 4Å:- Chain D: E.131, V.132
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.131
- Water bridges: D:V.132
EDO.51: 5 residues within 4Å:- Chain D: Y.10, L.171, R.174
- Chain E: E.131, V.132
4 PLIP interactions:2 interactions with chain E, 2 interactions with chain D- Hydrogen bonds: E:E.131, D:R.174, D:R.174
- Water bridges: E:V.132
EDO.52: 6 residues within 4Å:- Chain D: P.129, P.130, E.131, S.134, C.136, T.137
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:E.131, D:E.131, D:S.134, D:T.137
EDO.67: 6 residues within 4Å:- Chain E: P.129, P.130, E.131, S.134, C.136, T.137
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:E.128, E:E.131, E:E.131, E:S.134
- 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: ABDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BD
AE
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.42 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x QN8: (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)
- 4 x QNN: (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)
- 48 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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: ABDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BD
AE
B