Receptor
PDB id Resolution Class Description Source Keywords
5AOK 1.35 Å NON-ENZYME: BINDING STRUCTURE OF THE P53 CANCER MUTANT Y220C WITH BOUND SMALL MO PHIKAN7099 HOMO SAPIENS CELL CYCLE P53 CANCER TUMOR SUPPRESSION DNA BINDING CANTHERAPY SMALL-MOLECULE STABILIZERS MOLECULAR CHAPERONE
Ref.: EXPLOITING TRANSIENT PROTEIN STATES FOR THE DESIGN SMALL-MOLECULE STABILIZERS OF MUTANT P53. STRUCTURE V. 23 2246 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:1292;
A:1291;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
GOH B:1294;
A:1292;
 Valid;
Valid;
 none;
none;
 submit data
242.237 C11 H10 N6 O c1ccn...
ZN A:1313;
B:1300;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
PEG B:1293;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
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: GOH; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GOH 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: GOH; Similar ligands found: 33
No: Ligand Similarity coefficient
1 KLB 0.9396
2 1DZ 0.9293
3 ST4 0.9165
4 3E2 0.9026
5 DAN 0.9001
6 FIR 0.8995
7 KB8 0.8903
8 57Q 0.8890
9 7G5 0.8873
10 TNG 0.8862
11 ZO9 0.8855
12 FID 0.8843
13 YGL 0.8801
14 M2N 0.8799
15 P57 0.8752
16 ST6 0.8743
17 K5Z 0.8726
18 FSZ 0.8726
19 RF7 0.8716
20 TNF 0.8686
21 FIS 0.8685
22 1M1 0.8680
23 9GW 0.8657
24 YJD 0.8637
25 18F 0.8634
26 9UG 0.8628
27 T4E 0.8610
28 QC5 0.8603
29 WMR 0.8603
30 QVK 0.8601
31 1ZQ 0.8590
32 982 0.8586
33 UIH 0.8553
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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