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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 1443 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 1205 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 1039 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6MD; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 6MD 1 1
2 TT8 0.5875 0.830986
3 RAB 0.580645 0.952381
4 ADN 0.580645 0.952381
5 XYA 0.580645 0.952381
6 MTP 0.578125 0.895522
7 26A 0.569231 0.938462
8 6IA 0.518519 0.759494
9 1DA 0.5 0.952381
10 6C6 0.487805 0.753247
11 3DH 0.479452 0.865672
12 MTA 0.472222 0.893939
13 5N5 0.470588 0.921875
14 2SA 0.470588 0.776316
15 6CR 0.464789 0.869565
16 EP4 0.464789 0.867647
17 5CD 0.463768 0.876923
18 A4D 0.463768 0.921875
19 M2T 0.458333 0.842857
20 2FA 0.457143 0.882353
21 6K6 0.449438 0.819444
22 DTA 0.438356 0.826087
23 5AS 0.432099 0.705882
24 ABM 0.43038 0.833333
25 AMP 0.428571 0.805556
26 LMS 0.428571 0.707317
27 A 0.428571 0.805556
28 6RE 0.423077 0.794521
29 MHZ 0.421687 0.769231
30 IVH 0.414634 0.824324
31 IMO 0.4125 0.767123
32 A3N 0.4125 0.880597
33 J7C 0.4125 0.805556
34 ZAS 0.410256 0.802817
35 GJV 0.407407 0.783784
36 S4M 0.407407 0.779221
37 SRA 0.405063 0.763158
38 M33 0.404762 0.847222
39 MAO 0.402439 0.769231
40 NEC 0.4 0.863636
41 TBN 0.4 0.936508
42 AOC 0.4 0.865672
43 S7M 0.4 0.763158
44 DSH 0.4 0.805556
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: 189
This union binding pocket(no: 1) in the query (biounit: 4rdn.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5N5D SAM None
2 2ED4 FAD None
3 3S43 478 None
4 2FXD DR7 None
5 1I0S FMN 1.1976
6 1I0S NAP 1.1976
7 1L3I SAH 1.79641
8 2D37 FMN 1.79641
9 2D37 NAD 1.79641
10 2AAZ UMP 1.79641
11 1LSS NAD 2.14286
12 5FUI APY 2.27273
13 2HNK SAH 2.39521
14 4ZFL 4NK 2.39521
15 3L2B B4P 2.39521
16 4EWH T77 2.39521
17 1USF FMN 2.39521
18 1USF NAP 2.39521
19 1GZF NAD 2.39521
20 5CUO COA 2.99401
21 4F07 FAD 2.99401
22 5BW4 SAM 2.99401
23 1KOL NAD 2.99401
24 1WK8 VMS 2.99401
25 1U3D FAD 3.59281
26 4IVG ANP 3.59281
27 5T79 NDP 3.59281
28 6BSX GDP 3.59281
29 6BSX E7S 3.59281
30 1P0Z FLC 3.59281
31 3PPM JG1 3.59281
32 2FCR FMN 3.59281
33 3OEN GLU 3.59281
34 4KIB SAH 3.59281
35 2C6Q IMP 3.59281
36 3VC1 SAH 3.59281
37 3GFB NAD 3.59281
38 3GDH SAH 3.73444
39 2CJF RP4 3.82166
40 3CV3 UDP 4.19162
41 2RCU BUJ 4.19162
42 3LCC SAH 4.19162
43 2BII MTV 4.19162
44 2OI2 DP6 4.19162
45 1I1N SAH 4.19162
46 3A4T SFG 4.19162
47 3BGD SAH 4.19162
48 5EIN NAP 4.19162
49 2AOT SAH 4.19162
50 1QNF FAD 4.19162
51 4H8N NDP 4.19162
52 1CZI PRO PHI SMC NOR 4.19162
53 1JQD SAH 4.19162
54 4X9M FAD 4.79042
55 2PGJ N1C 4.79042
56 5V7I 8Z1 4.79042
57 1RVX SIA GAL NAG 4.79042
58 3GRU AMP 4.79042
59 5D2H AKG 4.79042
60 6F5Z SAH 4.79042
61 3B2Q AES 4.90405
62 1RZ1 FAD 4.96894
63 1WS5 MMA 5.26316
64 1KUJ MMA 5.26316
65 1UGY GLA BGC 5.26316
66 1UGY GLA GLC 5.26316
67 1WS4 AMG 5.26316
68 1TOQ AMG 5.26316
69 1UGW GAL 5.26316
70 1JAC AMG 5.26316
71 1WS4 GYP 5.26316
72 4OYA 1VE 5.38922
73 6ECU SAH 5.38922
74 1I8T FAD 5.38922
75 5KOK SAH 5.38922
76 3HQP FDP 5.38922
77 5B48 TDN 5.38922
78 1V7C HEY 5.38922
79 2IV2 2MD 5.38922
80 1EWY FAD 5.38922
81 4NBI D3Y 5.4878
82 1R27 MGD 5.98802
83 1YBH FAD 5.98802
84 2A9D MTE 5.98802
85 1KQF MGD 5.98802
86 2J8Z NAP 5.98802
87 5D9J 0N8 5.98802
88 3ZOD HQE 5.98802
89 3ZOD FMN 5.98802
90 5I35 ANP 5.98802
91 4JWF SAH 5.98802
92 3DCJ THH 5.98802
93 4DQL FAD 5.98802
94 4RJK TDL 5.98802
95 3DJF BC3 5.98802
96 2C42 TPP 6.58683
97 2C42 PYR 6.58683
98 4JK3 NAD 6.58683
99 2ZIF SAM 6.58683
100 2IVF MD1 6.58683
101 6B92 SAH 6.58683
102 1NV8 MEQ 6.58683
103 1NV8 SAM 6.58683
104 5L95 AMP 6.58683
105 4AR8 IP8 GLY PRO ALA 6.58683
106 2R5N RP5 6.58683
107 2R5N R5P 6.58683
108 3H8V ATP 6.58683
109 6GFK SAH 6.58683
110 5X62 SAH 6.58683
111 3KRB NAP 6.58683
112 1GPM CIT 6.85714
113 4M1U MBG A2G 7.14286
114 4M5P FMN 7.18563
115 2XTS MTE 7.18563
116 4JWH SAH 7.18563
117 1PL6 NAD 7.18563
118 1PL6 572 7.18563
119 1VJY 460 7.18563
120 6CDZ UMC 7.18563
121 1U1I NAD 7.18563
122 3G89 SAM 7.18563
123 3VHH VHH 7.31707
124 4ONQ SFG 7.78443
125 1X87 NAD 7.78443
126 1UWK NAD 7.78443
127 1UWK URO 7.78443
128 4RLQ 3SK 7.78443
129 5WS9 AMP 7.78443
130 1RZM E4P 7.78443
131 2P41 SAH 7.78443
132 4QNW FMN 7.78443
133 3S5W FAD 7.78443
134 2HSA FMN 7.78443
135 1O94 ADP 7.78443
136 5FA8 SAM 8.07453
137 1JG3 ADN 8.08511
138 1R18 SAH 8.38323
139 1P1C SAH 8.38323
140 3DUW SAH 8.38323
141 1HSK FAD 8.98204
142 3R4S SLB 8.98204
143 5EXE 5SR 8.98204
144 1NP7 FAD 8.98204
145 2ZKJ ADP 8.98204
146 5EFQ ADP 8.98204
147 4IPE ANP 8.98204
148 4NST ADP 8.98204
149 3WDM ADN 9.58084
150 3TLJ SAH 9.58084
151 1MOQ GLP 9.58084
152 4QTU SAM 9.58084
153 2NYA MGD 9.58084
154 2WZM NA7 9.58084
155 4AMV F6R 9.58084
156 3R6U CHT 10.1796
157 2IXB NAD 10.1796
158 1Y8Q ATP 10.1796
159 5M67 NAD 10.7784
160 1QAN SAH 11.0656
161 2PWY SAH 11.3772
162 3MB5 SAM 11.3772
163 4FZV SAM 11.3772
164 6DEN TP9 11.976
165 6DEN G8A 11.976
166 6DEN FAD 11.976
167 6EQS BV8 11.976
168 3O3R NAP 11.976
169 1T9D PYD 12.5749
170 1T9D 1MM 12.5749
171 1T9D P25 12.5749
172 1T9D FAD 12.5749
173 5WKC FAD 12.5749
174 2B7D C1B 13.1737
175 3CAQ NDP 13.1737
176 2BOS GLA GAL GLC NBU 13.2353
177 2BOS GLA GAL GLC 13.2353
178 2CHT TSA 13.3858
179 3IT7 TLA 13.7725
180 4RUS NDG 14.9701
181 1SOX MTE 14.9701
182 1DL5 SAH 15.5689
183 2BGS NDP 15.5689
184 2VPY MGD 16.1677
185 3NZW BOC TY5 ALA RE0 ABN 17.3653
186 4ZE0 VOR 17.3653
187 1XF1 CIT 22.1557
188 5FOM A2H 23.9521
189 5LD5 NAD 26.9461
Pocket No.: 2; Query (leader) PDB : 4RDN; Ligand: 6MD; Similar sites found with APoc: 77
This union binding pocket(no: 2) in the query (biounit: 4rdn.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1C4Q GLA GAL BGC None
2 3U2U UDP None
3 4GGZ BTN None
4 1UVC STE None
5 2PHX MAN MAN 1.1976
6 2PHU MAN MAN 1.1976
7 1Q8V MAN MAN 1.1976
8 1Q8S MAN MMA 1.1976
9 2GND MAN 1.1976
10 2PHT MAN MAN MAN 1.1976
11 1Q8O MAN MMA 1.1976
12 2AR6 NAG MAN 1.1976
13 2AUY NAG MAN MMA 1.1976
14 1Q8Q MAN MMA 1.1976
15 2PHT MAN MAN MAN BMA MAN 1.1976
16 2PHU MAN MAN MAN BMA MAN 1.1976
17 2PHW MAN MAN MAN BMA MAN MAN MAN 1.1976
18 2PHF MAN MAN BMA MAN 1.1976
19 2PHR MAN MAN 1.1976
20 1UKG MMA 1.1976
21 4UXH T5A 1.79641
22 3QV1 NAD 1.79641
23 1QH9 LAC 1.79641
24 4D7E FAD 2.39521
25 2IHU TP9 2.44328
26 5U97 PIT 2.99401
27 1Y0Y L2O VAL VAL ASP 2.99401
28 1RC0 KT5 2.99401
29 4K30 NLG 3.125
30 2B8T THM 3.59281
31 1W4R TTP 3.59281
32 5FUW QBT 3.59281
33 2RGO FAD 3.59281
34 5FUW THM 3.59281
35 4P8K FAD 4.19162
36 4P8K 38C 4.19162
37 3V91 UPG 4.19162
38 2Q16 ITT 4.19162
39 3BGD PM6 4.19162
40 3L4S NAD 4.79042
41 3H78 BE2 4.79042
42 4IJP 1EH 4.79042
43 1X9I G6Q 5.38922
44 5JFL NAD 5.38922
45 4DDY DN6 5.38922
46 2CXS F6P 5.98802
47 1TKB N1T 5.98802
48 5TWJ SAM 6.17284
49 2ORV 4TA 6.41026
50 5UAV TFB 6.58683
51 5UAV NDP 6.58683
52 1DNP FAD 6.58683
53 2HHJ 3PG 7.18563
54 2HHJ DG2 7.18563
55 1LL2 UPG 7.18563
56 1CER NAD 7.18563
57 3DZ6 M8E 7.78443
58 2ZJ3 G6P 7.78443
59 1LCK GLU GLY GLN PTR GLN PRO GLN PRO ALA 7.78443
60 3N7S 3N7 7.82609
61 3UOY FAD 8.38323
62 3UOY NAP 8.38323
63 2VYN NAD 9.58084
64 3ZM6 2GN 10.7784
65 5FJN FAD 10.7784
66 2Q4W FAD 10.7784
67 1KOJ PAN 11.3772
68 5HY1 WDL 11.3772
69 2Z6C FMN 11.6279
70 4NBU NAI 11.976
71 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 13.6842
72 5I39 FAD 14.3713
73 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 14.3713
74 3ZYR NAG NAG BMA MAN MAN NAG NAG 14.3713
75 1FLM FMN 14.7541
76 4RUS NAG 14.9701
77 2EJU SAH 17.9641
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