Receptor
PDB id Resolution Class Description Source Keywords
4RDN 2.1 Å NON-ENZYME: OTHER STRUCTURE OF YTH-YTHDF2 IN COMPLEX WITH M6A HOMO SAPIENS M6A METHYLATED RNA BINDING ATYPICAL BETA-PROPELLER RNA BINMETHYLATED RNA RNA BINDING PROTEIN
Ref.: STRUCTURE OF THE YTH DOMAIN OF HUMAN YTHDF2 IN COMP AN M(6)A MONONUCLEOTIDE REVEALS AN AROMATIC CAGE FO RECOGNITION. CELL RES. V. 24 1490 2014
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...
6MD B:601;
A:601;
Valid;
Valid;
none;
none;
submit data
281.268 C11 H15 N5 O4 CNc1c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RDN 2.1 Å NON-ENZYME: OTHER STRUCTURE OF YTH-YTHDF2 IN COMPLEX WITH M6A HOMO SAPIENS M6A METHYLATED RNA BINDING ATYPICAL BETA-PROPELLER RNA BINMETHYLATED RNA RNA BINDING PROTEIN
Ref.: STRUCTURE OF THE YTH DOMAIN OF HUMAN YTHDF2 IN COMP AN M(6)A MONONUCLEOTIDE REVEALS AN AROMATIC CAGE FO RECOGNITION. CELL RES. V. 24 1490 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6MD; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 6MD 1 1
2 6MZ 0.727273 0.84507
3 G 6MZ C 0.6 0.816901
4 TT8 0.5875 0.830986
5 RAB 0.580645 0.952381
6 ADN 0.580645 0.952381
7 XYA 0.580645 0.952381
8 MTP 0.578125 0.895522
9 26A 0.569231 0.938462
10 6IA 0.518519 0.759494
11 1DA 0.5 0.952381
12 6C6 0.487805 0.753247
13 ERJ 0.486486 0.90625
14 3DH 0.479452 0.865672
15 MTA 0.472222 0.893939
16 2SA 0.470588 0.776316
17 5N5 0.470588 0.921875
18 6MA 0.468354 0.76
19 6CR 0.464789 0.869565
20 EP4 0.464789 0.867647
21 5CD 0.463768 0.876923
22 A4D 0.463768 0.921875
23 NO7 0.45977 0.8
24 M2T 0.458333 0.842857
25 2FA 0.457143 0.882353
26 ERS 0.45679 0.842857
27 6K6 0.449438 0.819444
28 DTA 0.438356 0.826087
29 G G 6MZ C 0.438095 0.772152
30 HY8 0.435644 0.810811
31 ERP 0.433735 0.892308
32 5AS 0.432099 0.705882
33 45A 0.43038 0.833333
34 ABM 0.43038 0.833333
35 HZ2 0.43 0.810811
36 A 0.428571 0.805556
37 LMS 0.428571 0.707317
38 AMP 0.428571 0.805556
39 6RE 0.423077 0.794521
40 MHZ 0.421687 0.769231
41 IVH 0.414634 0.824324
42 A3N 0.4125 0.880597
43 IMO 0.4125 0.767123
44 J7C 0.4125 0.805556
45 ZAS 0.410256 0.802817
46 GJV 0.407407 0.783784
47 S4M 0.407407 0.779221
48 SRA 0.405063 0.763158
49 AMP MG 0.405063 0.816901
50 M33 0.404762 0.847222
51 MAO 0.402439 0.769231
52 S7M 0.4 0.763158
53 AOC 0.4 0.865672
54 TBN 0.4 0.936508
55 DSH 0.4 0.805556
56 NEC 0.4 0.863636
Similar Ligands (3D)
Ligand no: 1; Ligand: 6MD; Similar ligands found: 262
No: Ligand Similarity coefficient
1 NOS 0.9789
2 FM1 0.9749
3 GMP 0.9631
4 9DI 0.9622
5 FMC 0.9611
6 AD3 0.9610
7 NWW 0.9600
8 5AD 0.9599
9 Y3J 0.9592
10 FMB 0.9581
11 MDR 0.9565
12 3D1 0.9552
13 IMH 0.9542
14 5FD 0.9539
15 5ID 0.9528
16 TAL 0.9524
17 EKH 0.9523
18 UA2 0.9522
19 PRH 0.9511
20 FTU 0.9499
21 CL9 0.9482
22 HPR 0.9480
23 8OX 0.9472
24 F01 0.9465
25 DBM 0.9446
26 RPP 0.9442
27 ARJ 0.9440
28 NOC 0.9440
29 GNG 0.9439
30 NWQ 0.9427
31 MTH 0.9411
32 5NB 0.9395
33 5UD 0.9387
34 3AD 0.9382
35 3BH 0.9382
36 FM2 0.9371
37 5F1 0.9357
38 IMG 0.9348
39 CTN 0.9323
40 MTM 0.9308
41 5I5 0.9298
42 RFZ 0.9283
43 THM 0.9280
44 CFE 0.9278
45 MG7 0.9275
46 4UO 0.9274
47 7D7 0.9273
48 MTI 0.9267
49 URI 0.9254
50 PUR 0.9219
51 2FD 0.9191
52 DCF 0.9184
53 7CI 0.9159
54 0DN 0.9151
55 8HG 0.9132
56 3DT 0.9130
57 MCY 0.9124
58 MZR 0.9123
59 MCF 0.9115
60 3L1 0.9112
61 RBV 0.9109
62 ZJB 0.9109
63 5BT 0.9109
64 13A 0.9095
65 AFX 0.9068
66 SCT 0.9065
67 DUR 0.9064
68 B86 0.9063
69 NEO 0.9043
70 CDY 0.9037
71 CC5 0.9036
72 5AE 0.9031
73 XYP AHR 0.9025
74 HO4 0.9024
75 AHU 0.9022
76 2QU 0.9021
77 TMC 0.9021
78 Z57 0.9016
79 DCZ 0.9008
80 92O 0.8997
81 HBI 0.8990
82 GA2 0.8982
83 P2L 0.8975
84 UUA 0.8971
85 TO1 0.8969
86 H4B 0.8967
87 KF5 0.8966
88 DK4 0.8960
89 GPK 0.8944
90 5P7 0.8940
91 EXX 0.8936
92 DBS 0.8928
93 MPU 0.8925
94 EAT 0.8921
95 XYS XYP 0.8918
96 QQY 0.8918
97 KW7 0.8917
98 Z8B 0.8915
99 QQX 0.8914
100 TIA 0.8913
101 1KX 0.8908
102 H2B 0.8906
103 1KN 0.8901
104 NNR 0.8895
105 124 0.8894
106 E1N 0.8894
107 ACK 0.8888
108 Z21 0.8886
109 GEO 0.8882
110 H7S 0.8874
111 4AB 0.8871
112 XYP XYS 0.8871
113 NQ7 0.8869
114 RVD 0.8868
115 GAL FUC 0.8864
116 GLC 7LQ 0.8861
117 ZSP 0.8854
118 JMQ 0.8853
119 GPU 0.8853
120 GEN 0.8847
121 BHS 0.8847
122 GLC IFM 0.8846
123 47X 0.8843
124 5MD 0.8840
125 NEU 0.8837
126 THU 0.8837
127 XYP XDN 0.8831
128 0J4 0.8830
129 JA3 0.8829
130 1Q4 0.8824
131 SGP 0.8821
132 VUP 0.8820
133 MBY 0.8811
134 OLU 0.8811
135 7ZO 0.8808
136 JNW 0.8805
137 B5A 0.8804
138 XYP XYP 0.8799
139 AP6 0.8796
140 SGV 0.8785
141 0OK 0.8784
142 MGI 0.8784
143 XTS 0.8781
144 802 0.8777
145 DX6 0.8771
146 OA4 0.8768
147 DKX 0.8764
148 WCU 0.8761
149 Z15 0.8755
150 CJB 0.8747
151 DS8 0.8745
152 DKZ 0.8744
153 ACE TRP 0.8737
154 W23 0.8736
155 205 0.8735
156 BGC BGC 0.8735
157 XDL XYP 0.8734
158 7AP 0.8732
159 BIO 0.8732
160 B2L 0.8730
161 51Y 0.8728
162 XYS XYS 0.8727
163 6J3 0.8723
164 VIB 0.8722
165 7EH 0.8722
166 AWE 0.8722
167 KHP 0.8718
168 CTE 0.8717
169 DIH 0.8713
170 120 0.8712
171 TYU 0.8712
172 907 0.8711
173 9UL 0.8710
174 XIF XYP 0.8709
175 MI2 0.8708
176 7D1 MAN 0.8706
177 T1N 0.8705
178 7FZ 0.8703
179 NPS 0.8703
180 D64 0.8702
181 LVY 0.8701
182 AJ4 0.8699
183 7EL 0.8698
184 GLC DMJ 0.8697
185 15Q 0.8691
186 0GA 0.8690
187 XDN XYP 0.8688
188 54E 0.8686
189 7DE 0.8686
190 3RP 0.8685
191 XIL 0.8683
192 1FL 0.8680
193 JOB 0.8679
194 CR4 0.8678
195 RSV 0.8674
196 BMZ 0.8673
197 BBY 0.8672
198 EF2 0.8671
199 AUG 0.8669
200 0HY 0.8669
201 3DE 0.8667
202 6QT 0.8663
203 K80 0.8663
204 A4N 0.8662
205 8DA 0.8661
206 OVE 0.8661
207 334 0.8656
208 NPX 0.8656
209 6EL 0.8651
210 0J2 0.8650
211 XYP XIF 0.8648
212 BVD 0.8646
213 EZB 0.8642
214 JF8 0.8640
215 CJZ 0.8639
216 JFZ 0.8637
217 Y70 0.8636
218 M77 0.8633
219 2L1 0.8631
220 NXB 0.8629
221 TRP 0.8628
222 EI1 0.8625
223 B2X 0.8620
224 109 0.8618
225 F4U 0.8617
226 ISX 0.8612
227 Q8G 0.8612
228 6BK 0.8608
229 X2M 0.8603
230 801 0.8603
231 3WO 0.8602
232 3WN 0.8602
233 2QV 0.8600
234 AVX 0.8596
235 6JO 0.8593
236 U4J 0.8586
237 N5O 0.8583
238 FBC 0.8577
239 0DF 0.8575
240 9AA 0.8569
241 4YE 0.8569
242 FNT 0.8569
243 7L4 0.8569
244 A4T 0.8566
245 AUE 0.8566
246 9FH 0.8565
247 3Q0 0.8565
248 5E4 0.8561
249 QME 0.8560
250 HUX 0.8554
251 RVB 0.8552
252 DNB 0.8552
253 5XM 0.8551
254 C2M 0.8551
255 4NR 0.8548
256 MQU 0.8544
257 PQS 0.8537
258 NE2 0.8536
259 123 0.8529
260 TCL 0.8528
261 0QV 0.8518
262 CX5 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RDN; Ligand: 6MD; 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: 4rdn.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RDN; Ligand: 6MD; 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: 4rdn.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback