Receptor
PDB id Resolution Class Description Source Keywords
5TTW 1.74 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF EED IN COMPLEX WITH UNC4859 HOMO SAPIENS WD40 EED PEPTIDE INHIBITOR TRANSCRIPTION REGULATOR-INHIBITCOMPLEX
Ref.: DISCOVERY OF PEPTIDOMIMETIC LIGANDS OF EED AS ALLOS INHIBITORS OF PRC2. ACS COMB SCI V. 19 161 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX A:511;
A:505;
A:508;
C:510;
A:504;
C:507;
A:510;
C:508;
C:509;
A:502;
C:506;
C:505;
A:503;
A:509;
C:502;
A:506;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
n/a X *
UNX UNX C:503;
A:507;
D:101;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
n/a n/a
SO4 A:501;
C:501;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
PRO SER M3L PHE NLW D:1;
B:1;
 Valid;
Valid;
 Atoms found MORE than expected: % Diff = 1.267;
none;
 Kd = 1.09 uM
633.835 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6W7F 2.2 Å NON-ENZYME: OTHER STRUCTURE OF EED BOUND TO INHIBITOR 5285 HOMO SAPIENS INHIBITOR GENE REGULATION TRANSCRIPTION-INHIBITOR COMPLEX
Ref.: EEDI-5285: AN EXCEPTIONALLY POTENT, EFFICACIOUS, AN ACTIVE SMALL-MOLECULE INHIBITOR OF EMBRYONIC ECTODE DEVELOPMENT. J.MED.CHEM. V. 63 7252 2020
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6W7G ic50 = 0.5 nM Q3A C23 H22 F N5 O3 S Cc1ccc(c(n....
2 5U8A Ki = 13 nM 82D C22 H25 Br F N3 Cn1cc(c2c1....
3 6W7F ic50 = 0.2 nM Q3D C24 H22 F N5 O3 S CS(=O)(=O)....
4 5TTW Kd = 1.09 uM PRO SER M3L PHE NLW n/a n/a
5 5U69 Ki = 600 nM LQD C23 H29 N3 O Cn1cc(c2c1....
6 5U5H ic50 = 1.3 uM 7VV C18 H24 F N3 O CC(C)c1c2n....
7 3JZG - ALA ARG M3L SER n/a n/a
8 5U8F Ki = 11 nM 82G C24 H28 F N3 Cn1cc(c2c1....
9 5H13 ic50 = 11.58 uM LQA C25 H23 N3 O4 [H]/N=C1/C....
10 5U5K ic50 = 95 uM 7VY C13 H19 N O COc1cccc(c....
11 5U6D Ki = 2.6 nM 7XG C25 H30 F N5 O Cc1cccc(c1....
12 6SFB - L9K C21 H17 N5 O3 S CS(=O)(=O)....
13 6SFC Kd = 5.2 uM L9T C16 H16 N4 O2 S Cc1c(sc(n1....
14 3JZH - ASP PHE M3L THR ASP n/a n/a
15 3K27 - LYS GLN THR ALA ARG M3L SER THR GLY n/a n/a
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6W7G ic50 = 0.5 nM Q3A C23 H22 F N5 O3 S Cc1ccc(c(n....
2 5U8A Ki = 13 nM 82D C22 H25 Br F N3 Cn1cc(c2c1....
3 6W7F ic50 = 0.2 nM Q3D C24 H22 F N5 O3 S CS(=O)(=O)....
4 5TTW Kd = 1.09 uM PRO SER M3L PHE NLW n/a n/a
5 5U69 Ki = 600 nM LQD C23 H29 N3 O Cn1cc(c2c1....
6 5U5H ic50 = 1.3 uM 7VV C18 H24 F N3 O CC(C)c1c2n....
7 3JZG - ALA ARG M3L SER n/a n/a
8 5U8F Ki = 11 nM 82G C24 H28 F N3 Cn1cc(c2c1....
9 5H13 ic50 = 11.58 uM LQA C25 H23 N3 O4 [H]/N=C1/C....
10 5U5K ic50 = 95 uM 7VY C13 H19 N O COc1cccc(c....
11 5U6D Ki = 2.6 nM 7XG C25 H30 F N5 O Cc1cccc(c1....
12 6SFB - L9K C21 H17 N5 O3 S CS(=O)(=O)....
13 6SFC Kd = 5.2 uM L9T C16 H16 N4 O2 S Cc1c(sc(n1....
14 3JZH - ASP PHE M3L THR ASP n/a n/a
15 3K27 - LYS GLN THR ALA ARG M3L SER THR GLY n/a n/a
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6W7G ic50 = 0.5 nM Q3A C23 H22 F N5 O3 S Cc1ccc(c(n....
2 5U8A Ki = 13 nM 82D C22 H25 Br F N3 Cn1cc(c2c1....
3 6W7F ic50 = 0.2 nM Q3D C24 H22 F N5 O3 S CS(=O)(=O)....
4 5TTW Kd = 1.09 uM PRO SER M3L PHE NLW n/a n/a
5 5U69 Ki = 600 nM LQD C23 H29 N3 O Cn1cc(c2c1....
6 5U5H ic50 = 1.3 uM 7VV C18 H24 F N3 O CC(C)c1c2n....
7 3JZG - ALA ARG M3L SER n/a n/a
8 5U8F Ki = 11 nM 82G C24 H28 F N3 Cn1cc(c2c1....
9 5H13 ic50 = 11.58 uM LQA C25 H23 N3 O4 [H]/N=C1/C....
10 5U5K ic50 = 95 uM 7VY C13 H19 N O COc1cccc(c....
11 5U6D Ki = 2.6 nM 7XG C25 H30 F N5 O Cc1cccc(c1....
12 6SFB - L9K C21 H17 N5 O3 S CS(=O)(=O)....
13 6SFC Kd = 5.2 uM L9T C16 H16 N4 O2 S Cc1c(sc(n1....
14 3JZH - ASP PHE M3L THR ASP n/a n/a
15 3K27 - LYS GLN THR ALA ARG M3L SER THR GLY n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PRO SER M3L PHE NLW; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 PRO SER M3L PHE NLW 1 1
2 PRO GLN PHE SER LEU TRP LYS ARG 0.515385 0.764706
3 ARG PRO GLY ASN PHE LEU GLN SER SER PRO 0.503876 0.8125
4 THR PRO ASP TYR PHE LEU 0.491071 0.685714
5 ACE PHE ALA TYR M3L SER NH2 0.465517 0.823529
6 ARG PRO GLY ASN PHE PHE GLN SER ARG PRO 0.462687 0.680556
7 PRO SER ARG VAL 0.457944 0.695652
8 PRO LEU GLU PSA ARG LEU 0.451852 0.71831
9 PRO SER ARG TRP 0.447154 0.657534
10 GLY ASN PHE LEU GLN SER ARG 0.4375 0.661972
11 PRO ALA TRP LEU PHE GLU ALA 0.431655 0.681159
12 PRO LEU SER LYS 0.429907 0.793651
13 LEU PRO PRO PRO GLU SER GLU SER LYS VAL 0.421053 0.78125
14 PRO ALA PRO PHE ALA SER ALA 0.418605 0.818182
15 ASP PHE M3L THR ASP 0.416667 0.818182
16 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.413793 0.767123
17 PRO HIS PRO PHE HIS STA VAL ILE HIS LYS 0.407143 0.728571
Similar Ligands (3D)
Ligand no: 1; Ligand: PRO SER M3L PHE NLW; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6W7F; Ligand: Q3D; 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: 6w7f.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6W7F; Ligand: Q3D; 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: 6w7f.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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