Receptor
PDB id Resolution Class Description Source Keywords
5o1e 1.3 Å NON-ENZYME: BINDING P53 CANCER MUTANT Y220C IM COMPLEX WITH COMPOUND MB577 HOMO SAPIENS P53 TUMOR SUPPRESSOR CANCER MUTATION PROTEIN STABILIZATIOMOLECULE STABILIZERS CANCER THERAPY DNA BINDING PROTEIN CHAPERONES
Ref.: AMINOBENZOTHIAZOLE DERIVATIVES STABILIZE THE THERMO P53 CANCER MUTANT Y220C AND SHOW ANTICANCER ACTIVIT P53-Y220C CELL LINES. EUR J MED CHEM V. 152 101 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:404;
B:403;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
ZN A:401;
B:401;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
9GT A:402;
B:402;
 Valid;
Valid;
 none;
none;
 Kd = 33 uM
385.154 C14 H12 I N O4 C=CCO...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6SI3 1.4 Å NON-ENZYME: BINDING P53 CANCER MUTANT Y220S IN COMPLEX WITH SMALL-MOLECULE STABI PK9301 HOMO SAPIENS P53 TRANSCRIPTION FACTOR TUMOR SUPPRESSOR CANCER THERAPYONCOGENIC MUTANT PROTEIN MISFOLDING DNA-BINDING DOMAIN DSURFACE CREVICE SMALL-MOLECULE STABILIZER MUTANT P53 RESCBINDING PROTEIN
Ref.: TARGETING CAVITY-CREATING P53 CANCER MUTATIONS WITH SMALL-MOLECULE STABILIZERS: THE Y220X PARADIGM. ACS CHEM.BIOL. V. 15 657 2020
Members (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 105 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 6GGE - EYE C21 H23 N2 S CCn1c2ccc(....
5 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
6 5O1A Kd = 30 uM 9H5 C16 H17 I2 N3 O2 CN1CCN(CC1....
7 5G4O Kd = 37.2 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
8 5O1F Kd = 30 uM 9GQ C15 H16 I N O4 CCCCOc1cc(....
9 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
10 6GGF - EXQ C21 H23 N2 S CCn1c2ccc(....
11 5O1G Kd = 116 uM 9GK C19 H16 I N O4 c1ccc(cc1)....
12 5O1I Kd = 4 uM 9GH C16 H16 I N3 O3 S CCN(CC)c1n....
13 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
14 6GGC - EXN C20 H21 N2 O CCn1c2ccc(....
15 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
16 5O1D Kd = 22 uM 9GW C14 H14 I N O4 CCCOc1cc(c....
17 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
18 6SI4 Kd = 5.9 uM LEK C19 H19 N3 S CCn1c2ccc(....
19 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
20 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
21 6SI3 Kd = 4 uM LEB C16 H14 Br F3 N2 CNCc1ccc2c....
22 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
23 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
24 6GGD - EYB C19 H20 N3 O CCn1c2ccc(....
25 2VUK Kd = 125 uM P83 C16 H18 N2 CCn1c2cccc....
26 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
27 5O1E Kd = 33 uM 9GT C14 H12 I N O4 C=CCOc1cc(....
28 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
29 6GGA - EY2 C16 H18 Br N2 CCn1c2ccc(....
30 5O1B Kd = 20 uM 9H2 C11 H9 I2 N O2 c1ccn(c1)c....
31 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
32 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
33 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
34 5O1C Kd = 113 uM 9GZ C17 H11 F I N O3 c1ccn(c1)c....
35 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
36 6GGB - EXQ C21 H23 N2 S CCn1c2ccc(....
37 5O1H Kd = 14 uM 9GN C14 H14 I N O3 S CCCSc1cc(c....
38 4AGL Kd = 225 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
39 6SI0 Kd = 5.3 uM LEK C19 H19 N3 S CCn1c2ccc(....
40 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
70% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 105 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 6GGE - EYE C21 H23 N2 S CCn1c2ccc(....
5 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
6 5O1A Kd = 30 uM 9H5 C16 H17 I2 N3 O2 CN1CCN(CC1....
7 5G4O Kd = 37.2 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
8 5O1F Kd = 30 uM 9GQ C15 H16 I N O4 CCCCOc1cc(....
9 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
10 6GGF - EXQ C21 H23 N2 S CCn1c2ccc(....
11 5O1G Kd = 116 uM 9GK C19 H16 I N O4 c1ccc(cc1)....
12 5O1I Kd = 4 uM 9GH C16 H16 I N3 O3 S CCN(CC)c1n....
13 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
14 6GGC - EXN C20 H21 N2 O CCn1c2ccc(....
15 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
16 5O1D Kd = 22 uM 9GW C14 H14 I N O4 CCCOc1cc(c....
17 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
18 6SI4 Kd = 5.9 uM LEK C19 H19 N3 S CCn1c2ccc(....
19 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
20 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
21 6SI3 Kd = 4 uM LEB C16 H14 Br F3 N2 CNCc1ccc2c....
22 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
23 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
24 6GGD - EYB C19 H20 N3 O CCn1c2ccc(....
25 2VUK Kd = 125 uM P83 C16 H18 N2 CCn1c2cccc....
26 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
27 5O1E Kd = 33 uM 9GT C14 H12 I N O4 C=CCOc1cc(....
28 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
29 6GGA - EY2 C16 H18 Br N2 CCn1c2ccc(....
30 5O1B Kd = 20 uM 9H2 C11 H9 I2 N O2 c1ccn(c1)c....
31 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
32 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
33 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
34 5O1C Kd = 113 uM 9GZ C17 H11 F I N O3 c1ccn(c1)c....
35 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
36 6GGB - EXQ C21 H23 N2 S CCn1c2ccc(....
37 5O1H Kd = 14 uM 9GN C14 H14 I N O3 S CCCSc1cc(c....
38 4AGL Kd = 225 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
39 6SI0 Kd = 5.3 uM LEK C19 H19 N3 S CCn1c2ccc(....
40 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 105 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 6GGE - EYE C21 H23 N2 S CCn1c2ccc(....
5 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
6 5O1A Kd = 30 uM 9H5 C16 H17 I2 N3 O2 CN1CCN(CC1....
7 5G4O Kd = 37.2 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
8 5O1F Kd = 30 uM 9GQ C15 H16 I N O4 CCCCOc1cc(....
9 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
10 6GGF - EXQ C21 H23 N2 S CCn1c2ccc(....
11 5O1G Kd = 116 uM 9GK C19 H16 I N O4 c1ccc(cc1)....
12 5O1I Kd = 4 uM 9GH C16 H16 I N3 O3 S CCN(CC)c1n....
13 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
14 6GGC - EXN C20 H21 N2 O CCn1c2ccc(....
15 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
16 5O1D Kd = 22 uM 9GW C14 H14 I N O4 CCCOc1cc(c....
17 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
18 6SI4 Kd = 5.9 uM LEK C19 H19 N3 S CCn1c2ccc(....
19 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
20 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
21 6SI3 Kd = 4 uM LEB C16 H14 Br F3 N2 CNCc1ccc2c....
22 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
23 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
24 6GGD - EYB C19 H20 N3 O CCn1c2ccc(....
25 2VUK Kd = 125 uM P83 C16 H18 N2 CCn1c2cccc....
26 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
27 5O1E Kd = 33 uM 9GT C14 H12 I N O4 C=CCOc1cc(....
28 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
29 6GGA - EY2 C16 H18 Br N2 CCn1c2ccc(....
30 5O1B Kd = 20 uM 9H2 C11 H9 I2 N O2 c1ccn(c1)c....
31 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
32 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
33 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
34 5O1C Kd = 113 uM 9GZ C17 H11 F I N O3 c1ccn(c1)c....
35 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
36 6GGB - EXQ C21 H23 N2 S CCn1c2ccc(....
37 5O1H Kd = 14 uM 9GN C14 H14 I N O3 S CCCSc1cc(c....
38 4AGL Kd = 225 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
39 6SI0 Kd = 5.3 uM LEK C19 H19 N3 S CCn1c2ccc(....
40 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9GT; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 9GT 1 1
2 9GW 0.666667 0.872727
3 9GQ 0.646154 0.842105
4 9GK 0.591549 0.90566
5 Y0V 0.483871 0.86
6 9GN 0.418919 0.775862
7 9GZ 0.413333 0.826923
Similar Ligands (3D)
Ligand no: 1; Ligand: 9GT; Similar ligands found: 40
No: Ligand Similarity coefficient
1 DF4 0.9132
2 57Q 0.9107
3 DAN 0.9105
4 49A 0.9057
5 4AM 0.8986
6 9AM 0.8980
7 MAG 0.8960
8 E3M 0.8959
9 PK3 0.8919
10 SLB 0.8899
11 SIA 0.8895
12 0HX 0.8894
13 2MQ 0.8856
14 EQP 0.8846
15 2H8 0.8843
16 3C3 0.8826
17 GC9 0.8824
18 G39 0.8823
19 ZO9 0.8820
20 JY5 0.8817
21 9H2 0.8815
22 SNG 0.8811
23 3YW 0.8804
24 ST4 0.8799
25 ALH 0.8786
26 TZG 0.8764
27 AXP 0.8759
28 G28 0.8709
29 LZL 0.8708
30 ET 0.8676
31 NGE 0.8672
32 MKY 0.8641
33 M2N 0.8641
34 YGL 0.8636
35 VX3 0.8615
36 ST6 0.8601
37 YJD 0.8579
38 982 0.8570
39 KB8 0.8562
40 1ZQ 0.8544
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6SI3; Ligand: LEB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6si3.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6SI3; Ligand: LEB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6si3.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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