Receptor
PDB id Resolution Class Description Source Keywords
6T08 1.41 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF YTHDC1 WITH FRAGMENT 21 (DHU_DC1_131) HOMO SAPIENS FRAGMENT COMPLEX YTHDC1 EPITRANSCRIPTOMIC RNA BINDING PR
Ref.: SELECTIVELY DISRUPTING M6A-DEPENDENT PROTEIN-RNA INTERACTIONS WITH FRAGMENTS. ACS CHEM.BIOL. V. 15 618 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:602;
B:603;
A:602;
A:603;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
M5B B:601;
A:601;
 Valid;
Valid;
 none;
none;
 ic50 > 1000 uM
229.279 C7 H7 N3 O2 S2 c1cc(...
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: M5B; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 M5B 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: M5B; Similar ligands found: 87
No: Ligand Similarity coefficient
1 BZQ 0.9430
2 YTZ 0.9404
3 08D 0.9330
4 5TO 0.9314
5 7Y3 0.9262
6 6FR 0.9222
7 3VW 0.9213
8 1OH 0.9200
9 HSA 0.9192
10 11X 0.9192
11 6C5 0.9151
12 SFY 0.9121
13 M75 0.9110
14 HS7 0.9099
15 AVO 0.9091
16 H48 0.9042
17 GG8 0.9042
18 2OH 0.9040
19 VJP 0.9035
20 E8U 0.8996
21 OJD 0.8982
22 848 0.8963
23 RV1 0.8947
24 DY8 0.8943
25 E79 0.8938
26 5PV 0.8935
27 DI9 0.8929
28 KDG 0.8927
29 0UT 0.8922
30 PRO GLY 0.8919
31 5LD 0.8917
32 DA3 0.8916
33 DP4 0.8902
34 ALA GLU 0.8901
35 7UC 0.8898
36 27L 0.8889
37 5DL 0.8888
38 MYT 0.8886
39 4FP 0.8880
40 GVQ 0.8879
41 CCB 0.8874
42 ARG 0.8872
43 ASF 0.8865
44 6FG 0.8862
45 NBB 0.8847
46 NLG 0.8835
47 56D 0.8833
48 D4G 0.8827
49 TPM 0.8797
50 GVA 0.8795
51 EGV 0.8792
52 AHN 0.8773
53 HS6 0.8771
54 DED 0.8771
55 HAR 0.8769
56 CW6 0.8767
57 4TB 0.8753
58 FLC 0.8751
59 3GZ 0.8738
60 JFM 0.8731
61 3IP 0.8730
62 X1R 0.8727
63 1YO 0.8721
64 R5P 0.8703
65 ALA DGL 0.8702
66 HCA 0.8700
67 HJ7 0.8688
68 2JX 0.8686
69 7QD 0.8677
70 SB7 0.8664
71 0QA 0.8659
72 NQM 0.8659
73 ISC 0.8653
74 RE4 0.8648
75 2P3 0.8643
76 0OM 0.8642
77 AX5 0.8639
78 AOZ 0.8634
79 6JD 0.8628
80 GGG 0.8627
81 A5P 0.8584
82 M44 0.8575
83 GAE 0.8574
84 HL6 0.8574
85 B09 0.8572
86 1PC 0.8559
87 3H2 0.8545
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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