Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
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
P53_HUMAN
Ligand General Information  Top
Ligand Name Phosphonothreonine Ligand Info
Canonical SMILES CC(C(C(=O)O)N)OP(=O)(O)O
InChI 1S/C4H10NO6P/c1-2(3(5)4(6)7)11-12(8,9)10/h2-3H,5H2,1H3,(H,6,7)(H2,8,9,10)/t2-,3+/m1/s1
InChIKey USRGIUJOYOXOQJ-GBXIJSLDSA-N
PubChem Compound ID 3246323
Drug Binding Sites of Target  Top
PDB ID: 6RL3      Fragment AZ-003 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.30 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Residue
Distance (Å)
MET384
4.373
PHE385
3.393
LYS386
1.328
GLU388
1.318
Residue
Distance (Å)
GLY389
3.647
PRO390
4.762
ASP391
4.772
ASP393
4.394
PDB ID: 6RWU      Fragment AZ-010 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.46 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Residue
Distance (Å)
PHE385
3.436
LYS386
1.344
GLU388
1.346
Residue
Distance (Å)
GLY389
3.727
PRO390
4.829
ASP393
4.266
PDB ID: 6RWS      Fragment AZ-009 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.53 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Residue
Distance (Å)
MET384
4.944
PHE385
3.433
LYS386
1.355
GLU388
1.340
Residue
Distance (Å)
GLY389
3.776
PRO390
4.828
ASP393
4.304
PDB ID: 6RJZ      Fragment AZ-015 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.58 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.446
PHE385
3.322
LYS386
1.335
GLU388
1.326
Residue
Distance (Å)
GLY389
3.559
PRO390
4.817
ASP391
4.652
ASP393
4.283
PDB ID: 6RK8      Fragment AZ-014 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
MFKEGPD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.144
LYS386
1.330
GLU388
1.325
Residue
Distance (Å)
GLY389
3.768
PRO390
4.828
PDB ID: 6RL4      Fragment AZ-025 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.398
PHE385
3.211
LYS386
1.334
GLU388
1.325
Residue
Distance (Å)
GLY389
3.613
PRO390
4.752
ASP391
4.847
ASP393
4.367
PDB ID: 6RL6      Fragment AZ-024 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.351
PHE385
3.161
LYS386
1.334
GLU388
1.319
Residue
Distance (Å)
GLY389
3.714
PRO390
4.725
ASP391
4.836
ASP393
4.187
PDB ID: 6RM7      Fragment AZ-026 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.397
PHE385
3.229
LYS386
1.340
GLU388
1.324
Residue
Distance (Å)
GLY389
3.610
PRO390
4.828
ASP391
4.784
ASP393
4.352
PDB ID: 6SIO      Fragment AZ-017 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.410
LYS386
1.346
GLU388
1.321
Residue
Distance (Å)
GLY389
3.735
PRO390
4.845
ASP393
4.535
PDB ID: 6SIP      Fragment AZ-011 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.408
LYS386
1.336
GLU388
1.326
Residue
Distance (Å)
GLY389
3.679
PRO390
4.794
ASP393
4.317
PDB ID: 6SIQ      Fragment AZ-012 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
MFKEGPDSD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.354
LYS386
1.337
GLU388
1.320
Residue
Distance (Å)
GLY389
3.696
PRO390
4.799
ASP393
4.372
PDB ID: 6SIN      Fragment AZ-020 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.64 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.921
PHE385
3.414
LYS386
1.351
GLU388
1.319
Residue
Distance (Å)
GLY389
3.754
PRO390
4.998
ASP393
4.334
PDB ID: 6RWI      Fragment AZ-002 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.65 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.383
LYS386
1.304
GLU388
1.286
Residue
Distance (Å)
GLY389
3.676
PRO390
4.884
ASP393
4.394
PDB ID: 6RWH      Fragment AZ-007 binding at a primary and secondary binding site of the the p53pT387/14-3-3 sigma complex
Method X-ray diffraction Resolution 1.68 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.338
LYS386
1.337
GLU388
1.317
Residue
Distance (Å)
GLY389
3.734
ASP393
4.418
PDB ID: 6S9Q      Fragment AZ-004 binding at a primary and secondary site in a p53pT387/14-3-3 complex
Method X-ray diffraction Resolution 1.69 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.438
PHE385
3.086
LYS386
1.331
GLU388
1.327
Residue
Distance (Å)
GLY389
3.691
PRO390
4.742
ASP391
4.775
ASP393
4.369
PDB ID: 6RX2      Fragment AZ-005 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.82 Å Mutation No [1]
PDB Sequence
FKEGPD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.442
LYS386
1.305
GLU388
1.286
Residue
Distance (Å)
GLY389
3.543
PRO390
4.833
PDB ID: 6R5L      Fragment AZ-006 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.88 Å Mutation No [1]
PDB Sequence
KLMFKEGPD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.445
LYS386
1.332
GLU388
1.324
Residue
Distance (Å)
GLY389
3.655
PRO390
4.811
ASP391
4.981
PDB ID: 6RKI      Fragment AZ-023 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.88 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.488
LYS386
1.347
GLU388
1.335
Residue
Distance (Å)
GLY389
3.575
PRO390
4.743
ASP393
4.422
PDB ID: 6RKK      Fragment AZ-021 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.88 Å Mutation No [1]
PDB Sequence
KLMFKEGPD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.459
PHE385
3.111
LYS386
1.327
GLU388
1.321
Residue
Distance (Å)
GLY389
3.593
PRO390
4.658
ASP391
4.960
PDB ID: 6RKM      Fragment AZ-022 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.88 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.957
PHE385
3.382
LYS386
1.347
GLU388
1.327
Residue
Distance (Å)
GLY389
3.673
PRO390
4.860
ASP393
4.447
PDB ID: 6RM5      Fragment AZ-016 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.88 Å Mutation No [1]
PDB Sequence
LMFKEGP
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.539
PHE385
3.040
LYS386
1.332
Residue
Distance (Å)
GLU388
1.332
GLY389
3.675
PDB ID: 6S39      Fragment AZ-018 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.88 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.486
LYS386
1.337
GLU388
1.332
GLY389
3.584
Residue
Distance (Å)
PRO390
4.787
ASP391
4.725
ASP393
4.420
PDB ID: 6S40      Fragment AZ-001 binding at the p53pT387/14-3-3 sigma interface and additional sites
Method X-ray diffraction Resolution 1.90 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:393; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.476
LYS386
1.347
GLU388
1.334
Residue
Distance (Å)
GLY389
3.617
PRO390
4.768
ASP393
4.464
PDB ID: 6SLV      Fragment AZ-013 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 1.90 Å Mutation No [1]
PDB Sequence
KLMFKEGPDS
392
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:384 or .P:385 or .P:386 or .P:388 or .P:389 or .P:390 or .P:391 or .P:393; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET384
4.434
PHE385
3.212
LYS386
1.338
GLU388
1.324
Residue
Distance (Å)
GLY389
3.645
PRO390
4.779
ASP391
4.601
ASP393
4.470
PDB ID: 6S3C      Fragment AZ-019 binding at the p53pT387/14-3-3 sigma interface
Method X-ray diffraction Resolution 2.00 Å Mutation No [1]
PDB Sequence
KLMFKEGPD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .P:385 or .P:386 or .P:388 or .P:389 or .P:390; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE385
3.465
LYS386
1.350
GLU388
1.323
Residue
Distance (Å)
GLY389
3.530
PRO390
4.683
References  Top
REF 1 Fragment-based Differential Targeting of PPI Stabilizer Interfaces. J Med Chem. 2020 Jul 9;63(13):6694-6707.

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