Receptor
PDB id Resolution Class Description Source Keywords
6rt6 1.46 Å NON-ENZYME: OTHER THE YTH DOMAIN OF YTHDC1 PROTEIN IN COMPLEX WITH GGM6AC OLIGONUCLEOTIDE HOMO SAPIENS PROTEIN-RNA INTERACTION EPITRANSCRIPTOMICS RNA BINDING PRO
Ref.: FLEXIBLE BINDING OF M6A READER PROTEIN YTHDC1 TO IT PREFERRED RNA MOTIF. J CHEM THEORY COMPUT V. 15 7004 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 C:601;
C:603;
C:602;
B:601;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
G G 6MZ C E:1;
A:1;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.556;
Atoms found LESS than expected: % Diff = 0.733;
 Kd = 11.1 uM
585.447 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6RT7 1.73 Å NON-ENZYME: OTHER THE YTH DOMAIN OF YTHDC1 PROTEIN IN COMPLEX WITH GM6ACU OLIGONUCLEOTIDE HOMO SAPIENS PROTEIN-RNA INTERACTION EPITRANSCRIPTOMICS RNA BINDING PRO
Ref.: FLEXIBLE BINDING OF M6A READER PROTEIN YTHDC1 TO IT PREFERRED RNA MOTIF. J CHEM THEORY COMPUT V. 15 7004 2019
Members (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6T07 ic50 > 1000 uM M45 C6 H11 N5 c1nc([nH]n....
2 6SZ1 ic50 > 1000 uM M0W C9 H9 N3 CNc1c2cccc....
3 6T0O - M6N C8 H7 N3 O CC1=Nc2cnc....
4 6SZY ic50 > 1000 uM M5N C11 H16 N2 O CC(C)C1=NC....
5 6SYZ ic50 > 1000 uM M1E C7 H7 N3 S CNc1c2c(cc....
6 6RT5 - G 6MZ C n/a n/a
7 6T01 ic50 = 2057 uM M4B C11 H9 N3 O3 CC1=C(C(=N....
8 6SZ2 - M0Q C9 H9 N3 CNc1ccnc2c....
9 6SZN ic50 > 1000 uM YZM C8 H8 N2 O2 c1ccc(cc1)....
10 6T04 ic50 > 1000 uM M3H C9 H10 N2 c1ccc(cc1)....
11 6SZT ic50 = 1926 uM M4Q C11 H13 N3 O2 S CN(Cc1ccsc....
12 6T05 ic50 > 1000 uM M6H C10 H14 N2 c1ccc(cc1)....
13 6T0C Kd = 22 uM M4E C9 H9 N3 O CNC(=O)c1c....
14 6SZ7 ic50 = 1615 uM M1Q C8 H10 N2 O2 C1CCC2=NC(....
15 6T08 ic50 > 1000 uM M5B C7 H7 N3 O2 S2 c1cc(sc1)S....
16 6SZL ic50 > 1000 uM M3E C10 H8 N2 O2 c1ccc(cc1)....
17 6T11 ic50 = 402 uM O2A C10 H10 N2 O CNC(=O)c1c....
18 6T0Z ic50 > 1000 uM M75 C6 H9 N3 O2 S c1c(nc[nH]....
19 6SZX Kd = 58 uM M4K C15 H17 N3 O2 c1ccc(cc1)....
20 6T02 ic50 > 1000 uM M5E C11 H15 N O c1ccc(cc1)....
21 6RT4 - 6MZ C U n/a n/a
22 6T03 ic50 > 1000 uM MZY C3 H4 N2 S C1=CNC(=S)....
23 6RT7 Kd = 3.7 uM G 6MZ C U n/a n/a
24 6T0A ic50 = 2040 uM M58 C6 H8 N2 S c1cc(cnc1)....
25 6SZR ic50 > 1000 uM M3Z C13 H15 N3 O2 CN(Cc1cccc....
26 6T10 ic50 = 348 uM M6Z C9 H8 I N3 O CNC(=O)c1c....
27 6RT6 Kd = 11.1 uM G G 6MZ C n/a n/a
28 6SZ3 - M1H C10 H14 N2 CNc1ccnc2c....
29 6T0X ic50 > 1000 uM M6W C6 H12 N2 O CNC(=O)[C@....
30 6T06 ic50 = 2010 uM M5H C10 H12 N4 c1ccc2c(c1....
31 6SZ8 ic50 > 1000 uM M1Z C8 H11 N3 O2 C1CCN(C1)C....
32 6T12 ic50 = 825 uM M78 C12 H14 N2 O Cc1c([nH]c....
33 6T0D ic50 = 391 uM M4N C11 H11 N3 O CNC(=O)c1c....
34 6T09 - M4T C7 H8 N2 O CC(=O)Nc1c....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6T07 ic50 > 1000 uM M45 C6 H11 N5 c1nc([nH]n....
2 6SZ1 ic50 > 1000 uM M0W C9 H9 N3 CNc1c2cccc....
3 6T0O - M6N C8 H7 N3 O CC1=Nc2cnc....
4 6SZY ic50 > 1000 uM M5N C11 H16 N2 O CC(C)C1=NC....
5 6SYZ ic50 > 1000 uM M1E C7 H7 N3 S CNc1c2c(cc....
6 6RT5 - G 6MZ C n/a n/a
7 6T01 ic50 = 2057 uM M4B C11 H9 N3 O3 CC1=C(C(=N....
8 6SZ2 - M0Q C9 H9 N3 CNc1ccnc2c....
9 6SZN ic50 > 1000 uM YZM C8 H8 N2 O2 c1ccc(cc1)....
10 6T04 ic50 > 1000 uM M3H C9 H10 N2 c1ccc(cc1)....
11 6SZT ic50 = 1926 uM M4Q C11 H13 N3 O2 S CN(Cc1ccsc....
12 6T05 ic50 > 1000 uM M6H C10 H14 N2 c1ccc(cc1)....
13 6T0C Kd = 22 uM M4E C9 H9 N3 O CNC(=O)c1c....
14 6SZ7 ic50 = 1615 uM M1Q C8 H10 N2 O2 C1CCC2=NC(....
15 6T08 ic50 > 1000 uM M5B C7 H7 N3 O2 S2 c1cc(sc1)S....
16 6SZL ic50 > 1000 uM M3E C10 H8 N2 O2 c1ccc(cc1)....
17 6T11 ic50 = 402 uM O2A C10 H10 N2 O CNC(=O)c1c....
18 6T0Z ic50 > 1000 uM M75 C6 H9 N3 O2 S c1c(nc[nH]....
19 6SZX Kd = 58 uM M4K C15 H17 N3 O2 c1ccc(cc1)....
20 6T02 ic50 > 1000 uM M5E C11 H15 N O c1ccc(cc1)....
21 6RT4 - 6MZ C U n/a n/a
22 6T03 ic50 > 1000 uM MZY C3 H4 N2 S C1=CNC(=S)....
23 6RT7 Kd = 3.7 uM G 6MZ C U n/a n/a
24 6T0A ic50 = 2040 uM M58 C6 H8 N2 S c1cc(cnc1)....
25 6SZR ic50 > 1000 uM M3Z C13 H15 N3 O2 CN(Cc1cccc....
26 6T10 ic50 = 348 uM M6Z C9 H8 I N3 O CNC(=O)c1c....
27 6RT6 Kd = 11.1 uM G G 6MZ C n/a n/a
28 6SZ3 - M1H C10 H14 N2 CNc1ccnc2c....
29 6T0X ic50 > 1000 uM M6W C6 H12 N2 O CNC(=O)[C@....
30 6T06 ic50 = 2010 uM M5H C10 H12 N4 c1ccc2c(c1....
31 6SZ8 ic50 > 1000 uM M1Z C8 H11 N3 O2 C1CCN(C1)C....
32 6T12 ic50 = 825 uM M78 C12 H14 N2 O Cc1c([nH]c....
33 6T0D ic50 = 391 uM M4N C11 H11 N3 O CNC(=O)c1c....
34 6T09 - M4T C7 H8 N2 O CC(=O)Nc1c....
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6T07 ic50 > 1000 uM M45 C6 H11 N5 c1nc([nH]n....
2 6SZ1 ic50 > 1000 uM M0W C9 H9 N3 CNc1c2cccc....
3 6T0O - M6N C8 H7 N3 O CC1=Nc2cnc....
4 6SZY ic50 > 1000 uM M5N C11 H16 N2 O CC(C)C1=NC....
5 6SYZ ic50 > 1000 uM M1E C7 H7 N3 S CNc1c2c(cc....
6 6RT5 - G 6MZ C n/a n/a
7 6T01 ic50 = 2057 uM M4B C11 H9 N3 O3 CC1=C(C(=N....
8 6SZ2 - M0Q C9 H9 N3 CNc1ccnc2c....
9 6SZN ic50 > 1000 uM YZM C8 H8 N2 O2 c1ccc(cc1)....
10 6T04 ic50 > 1000 uM M3H C9 H10 N2 c1ccc(cc1)....
11 6SZT ic50 = 1926 uM M4Q C11 H13 N3 O2 S CN(Cc1ccsc....
12 6T05 ic50 > 1000 uM M6H C10 H14 N2 c1ccc(cc1)....
13 6T0C Kd = 22 uM M4E C9 H9 N3 O CNC(=O)c1c....
14 6SZ7 ic50 = 1615 uM M1Q C8 H10 N2 O2 C1CCC2=NC(....
15 6T08 ic50 > 1000 uM M5B C7 H7 N3 O2 S2 c1cc(sc1)S....
16 6SZL ic50 > 1000 uM M3E C10 H8 N2 O2 c1ccc(cc1)....
17 6T11 ic50 = 402 uM O2A C10 H10 N2 O CNC(=O)c1c....
18 6T0Z ic50 > 1000 uM M75 C6 H9 N3 O2 S c1c(nc[nH]....
19 6SZX Kd = 58 uM M4K C15 H17 N3 O2 c1ccc(cc1)....
20 6T02 ic50 > 1000 uM M5E C11 H15 N O c1ccc(cc1)....
21 6RT4 - 6MZ C U n/a n/a
22 6T03 ic50 > 1000 uM MZY C3 H4 N2 S C1=CNC(=S)....
23 6RT7 Kd = 3.7 uM G 6MZ C U n/a n/a
24 6T0A ic50 = 2040 uM M58 C6 H8 N2 S c1cc(cnc1)....
25 6SZR ic50 > 1000 uM M3Z C13 H15 N3 O2 CN(Cc1cccc....
26 6T10 ic50 = 348 uM M6Z C9 H8 I N3 O CNC(=O)c1c....
27 6RT6 Kd = 11.1 uM G G 6MZ C n/a n/a
28 6SZ3 - M1H C10 H14 N2 CNc1ccnc2c....
29 6T0X ic50 > 1000 uM M6W C6 H12 N2 O CNC(=O)[C@....
30 6T06 ic50 = 2010 uM M5H C10 H12 N4 c1ccc2c(c1....
31 6SZ8 ic50 > 1000 uM M1Z C8 H11 N3 O2 C1CCN(C1)C....
32 6T12 ic50 = 825 uM M78 C12 H14 N2 O Cc1c([nH]c....
33 6T0D ic50 = 391 uM M4N C11 H11 N3 O CNC(=O)c1c....
34 6T09 - M4T C7 H8 N2 O CC(=O)Nc1c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: G G 6MZ C ; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 G G 6MZ C 1 1
2 6MZ C U 0.818182 1
3 G 6MZ C U 0.748031 0.987179
4 G C 0.647541 0.925926
5 G 6MZ C 0.550459 0.858974
6 CDP MG 0.528302 0.858974
7 C5P 0.5 0.825
8 CAR 0.5 0.825
9 C 0.5 0.825
10 6MZ 0.495413 0.8375
11 CDP 0.486239 0.814815
12 7XL 0.482456 0.817073
13 CDP RB0 0.463415 0.839506
14 HF4 0.460177 0.814815
15 CTP 0.460177 0.814815
16 C5G 0.459016 0.839506
17 C2G 0.457627 0.82716
18 0RC 0.456897 0.797619
19 CDC 0.454545 0.784091
20 G 5MC C U 0.453988 0.892857
21 ATP A 0.453125 0.884615
22 ATP A A A 0.453125 0.884615
23 2TM 0.452174 0.785714
24 GPC 0.446809 0.860465
25 CDM 0.439024 0.8
26 OMC OMU OMG OMG U 0.43871 0.939024
27 6MD 0.438095 0.772152
28 CSV 0.4375 0.829268
29 CSQ 0.4375 0.829268
30 CTN 0.431373 0.759494
31 AR3 0.431373 0.759494
32 C3P 0.422018 0.8125
33 CXY 0.420635 0.817073
34 2AA 0.408451 0.732673
35 APU 0.407143 0.9
36 A3P 0.401709 0.825
37 C5P SIA 0.4 0.864198
Similar Ligands (3D)
Ligand no: 1; Ligand: G G 6MZ C ; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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