SMTL ID : 7b49.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 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.17: 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.37: 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 ZN.53: 4 residues within 4Å: Chain E: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.83, E:H.86, E:C.145, E:C.149

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 PLIP FMT.5: 3 residues within 4Å: Chain A: R.155 Chain C: G.8, C.9 Ligand excluded by PLIP FMT.6: 2 residues within 4Å: Chain A: K.71, Q.72 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: Y.112, L.113, D.114 Ligand excluded by PLIP FMT.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 PLIP FMT.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 PLIP FMT.10: 5 residues within 4Å: Chain A: R.17, W.53, V.54, D.55, D.135 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: E.128, T.137, T.138, I.139 Ligand excluded by PLIP FMT.12: 5 residues within 4Å: Chain A: D.93, R.103, V.104, E.105, N.142 Ligand excluded by PLIP FMT.20: 5 residues within 4Å: Chain B: R.17, L.18, G.19, W.53 Ligands: ACT.30 Ligand excluded by PLIP FMT.21: 2 residues within 4Å: Chain B: K.71, Q.72 Ligand excluded by PLIP FMT.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 PLIP FMT.23: 3 residues within 4Å: Chain B: Y.112, L.113, D.114 Ligand excluded by PLIP FMT.24: 3 residues within 4Å: Chain B: R.155 Chain C: G.18, C.19 Ligand excluded by PLIP FMT.25: 5 residues within 4Å: Chain B: S.73, Q.74, H.75, M.76, T.77 Ligand excluded by PLIP FMT.26: 5 residues within 4Å: Chain B: H.180, D.188, T.191, E.192 Chain F: T.7 Ligand excluded by PLIP FMT.27: 5 residues within 4Å: Chain B: R.17, W.53, V.54, D.55, D.135 Ligand excluded by PLIP FMT.28: 5 residues within 4Å: Chain B: N.107, E.128, T.137, T.138, I.139 Ligand excluded by PLIP FMT.29: 5 residues within 4Å: Chain B: D.93, R.103, V.104, E.105, N.142 Ligand excluded by PLIP FMT.32: 3 residues within 4Å: Chain C: A.6, T.7 Ligands: FMT.36 Ligand excluded by PLIP FMT.33: 3 residues within 4Å: Chain C: A.16, T.17 Chain D: T.191 Ligand excluded by PLIP FMT.34: 5 residues within 4Å: Chain C: T.17 Chain D: H.180, D.188, T.191, E.192 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain C: T.17 Chain F: G.4, C.5 Ligand excluded by PLIP FMT.36: 4 residues within 4Å: Chain C: T.7 Chain F: G.14, C.15 Ligands: FMT.32 Ligand excluded by PLIP FMT.40: 5 residues within 4Å: Chain D: R.17, L.18, G.19, W.53 Ligands: ACT.49 Ligand excluded by PLIP FMT.41: 3 residues within 4Å: Chain D: R.155 Chain F: G.8, C.9 Ligand excluded by PLIP FMT.42: 2 residues within 4Å: Chain D: K.71, Q.72 Ligand excluded by PLIP FMT.43: 3 residues within 4Å: Chain D: Y.112, L.113, D.114 Ligand excluded by PLIP FMT.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 PLIP FMT.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 PLIP FMT.46: 5 residues within 4Å: Chain D: R.17, W.53, V.54, D.55, D.135 Ligand excluded by PLIP FMT.47: 4 residues within 4Å: Chain D: E.128, T.137, T.138, I.139 Ligand excluded by PLIP FMT.48: 5 residues within 4Å: Chain D: D.93, R.103, V.104, E.105, N.142 Ligand excluded by PLIP FMT.56: 5 residues within 4Å: Chain E: R.17, L.18, G.19, W.53 Ligands: ACT.66 Ligand excluded by PLIP FMT.57: 2 residues within 4Å: Chain E: K.71, Q.72 Ligand excluded by PLIP FMT.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 PLIP FMT.59: 3 residues within 4Å: Chain E: Y.112, L.113, D.114 Ligand excluded by PLIP FMT.60: 3 residues within 4Å: Chain E: R.155 Chain F: G.18, C.19 Ligand excluded by PLIP FMT.61: 5 residues within 4Å: Chain E: S.73, Q.74, H.75, M.76, T.77 Ligand excluded by PLIP FMT.62: 5 residues within 4Å: Chain C: T.7 Chain E: H.180, D.188, T.191, E.192 Ligand excluded by PLIP FMT.63: 5 residues within 4Å: Chain E: R.17, W.53, V.54, D.55, D.135 Ligand excluded by PLIP FMT.64: 5 residues within 4Å: Chain E: N.107, E.128, T.137, T.138, I.139 Ligand excluded by PLIP FMT.65: 5 residues within 4Å: Chain E: D.93, R.103, V.104, E.105, N.142 Ligand excluded by PLIP FMT.68: 3 residues within 4Å: Chain F: A.6, T.7 Ligands: FMT.72 Ligand excluded by PLIP FMT.69: 3 residues within 4Å: Chain A: T.191 Chain F: A.16, T.17 Ligand excluded by PLIP FMT.70: 5 residues within 4Å: Chain A: H.180, D.188, T.191, E.192 Chain F: T.17 Ligand excluded by PLIP FMT.71: 3 residues within 4Å: Chain C: G.4, C.5 Chain F: T.17 Ligand excluded by PLIP FMT.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: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:V.132 Hydrogen bonds: A:R.174, A:R.174 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

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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
A

B
B

D
A

E
B

Cellular tumor antigen p53

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