Receptor
PDB id Resolution Class Description Source Keywords
6T01 1.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF YTHDC1 WITH FRAGMENT 13 (DHU_DC1_153) 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;
A:602;
B:604;
B:603;
A:604;
A:603;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
M4B B:601;
A:601;
 Valid;
Valid;
 none;
none;
 ic50 = 2057 uM
231.207 C11 H9 N3 O3 CC1=C...
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: M4B; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 M4B 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: M4B; Similar ligands found: 146
No: Ligand Similarity coefficient
1 A1Y 0.9489
2 QZ8 0.9374
3 61O 0.9314
4 977 0.9312
5 A9O 0.9298
6 K3Y 0.9253
7 96R 0.9249
8 BPS 0.9238
9 1FF 0.9231
10 25O 0.9230
11 89J 0.9221
12 8WZ 0.9220
13 SQP 0.9159
14 60Q 0.9142
15 B4O 0.9099
16 11G 0.9094
17 JUO 0.9090
18 OBP 0.9083
19 2LX 0.9066
20 GRX 0.9056
21 49N 0.9048
22 6J9 0.9047
23 BCK 0.9037
24 B2Y 0.9031
25 OX2 0.9029
26 LT8 0.9027
27 TQU 0.9024
28 4MX 0.9018
29 CMU 0.9011
30 A3K 0.9010
31 A9P 0.9006
32 S0G 0.9004
33 JAK 0.8994
34 8GK 0.8992
35 YO5 0.8990
36 CC5 0.8985
37 XFE 0.8972
38 5OF 0.8963
39 1XA 0.8962
40 C93 0.8959
41 DC5 0.8955
42 XZ8 0.8955
43 A3Q 0.8952
44 NBG 0.8938
45 6HX 0.8933
46 3WJ 0.8924
47 PVK 0.8919
48 OUB 0.8919
49 NLA 0.8918
50 IBM 0.8917
51 PVQ 0.8916
52 NZ3 0.8915
53 4GP 0.8912
54 CGW 0.8908
55 SYR 0.8907
56 GL7 0.8906
57 1Z8 0.8906
58 CR1 0.8904
59 S3B 0.8900
60 49O 0.8890
61 9GP 0.8878
62 S7B 0.8874
63 QMS 0.8870
64 CLU 0.8851
65 AED 0.8848
66 6XI 0.8848
67 JR2 0.8847
68 5NS 0.8844
69 SLY 0.8843
70 CPW 0.8830
71 67Y 0.8828
72 T6Z 0.8818
73 PW1 0.8811
74 512 0.8802
75 KFN 0.8795
76 0Q2 0.8793
77 N8Z 0.8792
78 ZYW 0.8780
79 CP6 0.8777
80 22L 0.8772
81 ELH 0.8764
82 G6P 0.8761
83 BY5 0.8760
84 NTF 0.8760
85 SQ4 0.8759
86 5M8 0.8759
87 AIN 0.8758
88 PYU 0.8753
89 HPT 0.8752
90 CP7 0.8751
91 DKZ 0.8746
92 2AN 0.8742
93 SV4 0.8741
94 MEX 0.8740
95 RUG 0.8739
96 LOG 0.8737
97 9KH 0.8737
98 CG8 0.8735
99 S3C 0.8722
100 KF5 0.8720
101 57O 0.8720
102 ABJ 0.8717
103 29Q 0.8716
104 G1P 0.8714
105 OA3 0.8712
106 6HP 0.8711
107 NPL 0.8706
108 6DP 0.8705
109 SQ7 0.8701
110 CJB 0.8693
111 DKX 0.8693
112 A7K 0.8688
113 982 0.8688
114 AZC 0.8687
115 AC2 0.8684
116 56N 0.8680
117 AKD 0.8675
118 GF4 0.8672
119 PLP 0.8666
120 LIP 0.8662
121 KZ9 0.8655
122 M3Q 0.8654
123 IPD 0.8654
124 AYS 0.8651
125 1M4 0.8637
126 3JM 0.8635
127 DIF 0.8631
128 CTN 0.8631
129 9F8 0.8627
130 IPT 0.8626
131 FA6 0.8624
132 5WU 0.8624
133 1CY 0.8620
134 JTH 0.8619
135 6GP 0.8611
136 KDM 0.8594
137 TNF 0.8592
138 GFE 0.8569
139 FXH 0.8548
140 4ME 0.8544
141 F95 0.8541
142 3GC 0.8540
143 EGR 0.8536
144 SNG 0.8516
145 AB3 0.8516
146 AMR 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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