Receptor
PDB id Resolution Class Description Source Keywords
4AGM 1.52 Å NON-ENZYME: BINDING STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO THE S SMALL MOLECULE PHIKAN5086 HOMO SAPIENS TRANSCRIPTION CELL CYCLE APOPTOSIS CANCER MUTATION SURFACREVICE PROTEIN FOLDING AGGREGATION MUTANT RESCUE SMALLDRUG PROTEIN STABILIZATION HALOGEN BONDING ZINC BINDING
Ref.: HALOGEN-ENRICHED FRAGMENT LIBRARIES AS LEADS FOR DR OF MUTANT P53. J.AM.CHEM.SOC. V. 134 6810 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
P86 A:400;
B:400;
 Valid;
Valid;
 none;
none;
 Kd = 105 uM
514.184 C16 H24 I2 N2 O CCN(C...
ZN A:1300;
B:1300;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
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: P86; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 P86 1 1
2 NXG 0.588235 0.892857
3 P96 0.493827 0.877193
4 P51 0.487805 0.892857
5 P74 0.481928 0.746269
6 P84 0.426471 0.942308
Similar Ligands (3D)
Ligand no: 1; Ligand: P86; Similar ligands found: 7
No: Ligand Similarity coefficient
1 UL7 0.9068
2 QTJ 0.8896
3 U55 0.8850
4 MGI 0.8827
5 CT7 0.8723
6 HGK 0.8651
7 MBE 0.8602
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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