Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T15739 | Target Info | |||
| Target Name | Cellular tumor antigen p53 (TP53) | ||||
| Synonyms | Tumor suppressor p53; Phosphoprotein p53; P53; Antigen NY-CO-13 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | TP53 | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | (2S)-2-methyl-1-azabicyclo[2.2.2]octan-3-one | Ligand Info | |||
| Canonical SMILES | CC1C(=O)C2CCN1CC2 | ||||
| InChI | 1S/C8H13NO/c1-6-8(10)7-2-4-9(6)5-3-7/h6-7H,2-5H2,1H3/t6-/m0/s1 | ||||
| InChIKey | LGOHLIRGPFPGKT-LURJTMIESA-N | ||||
| PubChem Compound ID | 93514108 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7B4N 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) | ||||||
| Method | X-ray diffraction | Resolution | 1.32 Å | Mutation | No | [1] |
| PDB Sequence |
SSSVPSQKTY
103 QGSYGFRLGF113 LHSAKVTCTY126 SPALNKMFCQ136 LAKTCPVQLW146 VDSTPPPGTR 156 VRAMAIYKQS166 QHMTEVVRRC176 PHHERCLAPP191 QHLIRVEGNL201 RVEYLDDRNT 211 FRHSVVVPYE221 PPEVGSDCTT231 IHYNYMCNSS241 CMGGMNRRPI251 LTIITLEDSS 261 GNLLGRNSFE271 VRVCACPGRD281 RRTEEENLRK291 KG
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| PDB ID: 7B4H 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 (III) | ||||||
| Method | X-ray diffraction | Resolution | 1.39 Å | Mutation | No | [1] |
| PDB Sequence |
SSSVPSQKTY
103 QGSYGFRLGF113 LHSKSVTCTY126 SPALNKMFCQ136 LAKTCPVQLW146 VDSTPPPGTR 156 VRAMAIYKQS166 QHMTEVVRRC176 PHHERCSGLA189 PPQHLIRVEG199 NLRVEYLDDR 209 NTFRHSVVVP219 YEPPEVGSDC229 TTIHYNYMCN239 SSCMGGMNRR249 PILTIITLED 259 SSGNLLGRNS269 FEVRVCACPG279 RDRRTEEENL289 RKKG
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| PDB ID: 7B49 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 | ||||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | Yes | [1] |
| PDB Sequence |
SSSVPSQKTY
103 QGSYGFRLGF113 LHAKSVTCTY126 SPALNKMFCQ136 LAKTCPVQLW146 VDSTPPPGTR 156 VRAMAIYKQS166 QHMTEVVRRC176 PHHERCSDGL188 APPQHLIRVE198 GNLRVEYLDD 208 RNTFRHSVVV218 PYEPPEVGSD228 CTTIHYNYMC238 NSSCMGGMNR248 RPILTIITLE 258 DSSGNLLGRN268 SFEVHVCACP278 GRDRRTEEEN288 LRKKG
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| PDB ID: 7B4E 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 | ||||||
| Method | X-ray diffraction | Resolution | 1.58 Å | Mutation | Yes | [1] |
| PDB Sequence |
SSSVPSQKTY
103 QGSYGFRLGF113 VTCTYSPALN131 KMFCQLAKTC141 PVQLWVDSTP151 PPGTRVRAMA 161 IYKQSQHMTE171 VVRRCPHHER181 CSDGLAPPQH193 LIRVEGNLRV203 EYLDDRNTFR 213 HSVVVPYEPP223 EVGSDCTTIH233 YNYMCNSSCM243 GGMNRRPILT253 IITLEDSSGN 263 LLGRNSFEVR273 VCACPGRDWR283 TEEENLRKKG293
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QNN or .QNN2 or .QNN3 or :3QNN;style chemicals stick;color identity;select .A:136 or .A:276 or .A:277; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6ZNC 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 (I) | ||||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [1] |
| PDB Sequence |
SSSVPSQKTY
103 QGSYGFRLGF113 LHSGTAKSVT123 CTYSPALNKM133 FCQLAKTCPV143 QLWVDSTPPP 153 GTRVRAMAIY163 KQSQHMTEVV173 RRCPHHERCL188 APPQHLIRVE198 GNLRVEYLDD 208 RNTFRHSVVV218 PYEPPEVSDC229 TTIHYNYMCN239 SSCMGGMNRR249 PILTIITLED 259 SSGNLLGRNS269 FEVRVCACPG279 RDRRTEEENL289 RKKG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QNN or .QNN2 or .QNN3 or :3QNN;style chemicals stick;color identity;select .A:114 or .A:115 or .A:116 or .A:120 or .A:121 or .A:123 or .A:124 or .A:125 or .A:136 or .A:140 or .A:142 or .A:144 or .A:146 or .A:227 or .A:228 or .A:229 or .A:231 or .A:276 or .A:277; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7B4C Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C mutant bound to MQ: R273C-MQ (II) | ||||||
| Method | X-ray diffraction | Resolution | 1.71 Å | Mutation | Yes | [1] |
| PDB Sequence |
SVPSQKTYQG
105 SYGFRLGFLH115 SGTAKSVTCT125 YSPALNKMFC135 QLAKTCPVQL145 WVDSTPPPGT 155 RVRAMAIYKQ165 SQHMTEVVRR175 CPHHERDSDG187 LAPPQHLIRV197 EGNLRVEYLD 207 DRNTFRHSVV217 VPYEPPEVGS227 DCTTIHYNYM237 CNSSCMGGMN247 RRPILTIITL 257 EDSSGNLLGR267 NSFEVCVCAC277 PGRDRRTEEE287 N
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QNN or .QNN2 or .QNN3 or :3QNN;style chemicals stick;color identity;select .A:132 or .A:240 or .A:241 or .A:248 or .A:249 or .A:250 or .A:271 or .A:272 or .A:273 or .A:274 or .A:285; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7B4B Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C mutant bound to MQ: R273C-MQ (I) | ||||||
| Method | X-ray diffraction | Resolution | 1.76 Å | Mutation | Yes | [1] |
| PDB Sequence |
VPSQKTYQGS
106 YGFRLGFLHS116 GTAKSVTCTY126 SPALNKMFCQ136 LAKTCPVQLW146 VDSTPPPGTR 156 VRAMAIYKQS166 QHMTEVVRRC176 PHHERCDGLA189 PPQHLIRVEG199 NLRVEYLDDR 209 NTFRHSVVVP219 YEPPEVGSDC229 TTIHYNYMCN239 SSCMGGMNRR249 PILTIITLED 259 SSGNLLGRNS269 FEVCVCACPG279 RDRRTEEENL289
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QNN or .QNN2 or .QNN3 or :3QNN;style chemicals stick;color identity;select .A:132 or .A:240 or .A:248 or .A:249 or .A:250 or .A:272 or .A:273 or .A:274 or .A:285; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7B4D 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 | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [1] |
| PDB Sequence |
SSSVPSQKTY
103 QGSYGFRLGF113 LHSGTAKSVT123 CTYSPALNKM133 FCQLAKTCPV143 QLWVDSTPPP 153 GTRVRAMAIY163 KQSQHMTEVV173 RRCPHHERCD186 GLAPPQHLIR196 VEGNLRVEYL 206 DDRNTFRHSV216 VVPYEPPEVG226 SDCTTIHYNY236 MCNRSCMGGM246 NRRPILTIIT 256 LEDSSGNLLG266 RNSFEVCVCA276 CPGRDRRTEE286 ENLRKKG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QNN or .QNN2 or .QNN3 or :3QNN;style chemicals stick;color identity;select .A:114 or .A:115 or .A:116 or .A:120 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125 or .A:136 or .A:140 or .A:142 or .A:144 or .A:146 or .A:227 or .A:228 or .A:229 or .A:231 or .A:276 or .A:277; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU114
3.602
HIS115
4.643
SER116
3.740
LYS120
3.408
SER121
3.674
VAL122
3.953
THR123
3.645
CYS124
1.804
THR125
4.817
GLN136
3.624
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Nat Commun. 2021 Dec 3;12(1):7057. | ||||
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