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 1256 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 1068 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 922 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 XYA 0.580645 0.952381
4 ADN 0.580645 0.952381
5 RAB 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 A4D 0.463768 0.921875
18 5CD 0.463768 0.876923
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 A 0.428571 0.805556
27 6RE 0.423077 0.794521
28 MHZ 0.421687 0.769231
29 IVH 0.414634 0.824324
30 IMO 0.4125 0.767123
31 J7C 0.4125 0.805556
32 A3N 0.4125 0.880597
33 ZAS 0.410256 0.802817
34 S4M 0.407407 0.779221
35 GJV 0.407407 0.783784
36 SRA 0.405063 0.763158
37 M33 0.404762 0.847222
38 MAO 0.402439 0.769231
39 AMP MG 0.4 0.783784
40 AOC 0.4 0.865672
41 S7M 0.4 0.763158
42 DSH 0.4 0.805556
43 TBN 0.4 0.936508
44 NEC 0.4 0.863636
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RDN; Ligand: 6MD; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 4rdn.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5N5D SAM 0.01723 0.41306 None
2 3S43 478 0.03982 0.40432 None
3 2FXD DR7 0.0421 0.4029 None
4 2D37 FMN 0.01129 0.43134 1.79641
5 2D37 NAD 0.01196 0.43134 1.79641
6 3L2B B4P 0.03247 0.41267 2.39521
7 1GZF NAD 0.03085 0.40185 2.39521
8 5CUO COA 0.00954 0.42584 2.99401
9 5BW4 SAM 0.01882 0.40842 2.99401
10 1WK8 VMS 0.01543 0.40387 2.99401
11 1P0Z FLC 0.004544 0.42311 3.59281
12 2FCR FMN 0.01891 0.4057 3.59281
13 4KIB SAH 0.0247 0.40134 3.59281
14 2RCU BUJ 0.02162 0.43876 4.19162
15 3LCC SAH 0.0103 0.42178 4.19162
16 1I1N SAH 0.02678 0.41159 4.19162
17 2AOT SAH 0.01901 0.40575 4.19162
18 1CZI PRO PHI SMC NOR 0.03139 0.40262 4.19162
19 4X9M FAD 0.03929 0.41654 4.79042
20 1RVX SIA GAL NAG 0.01181 0.41104 4.79042
21 3GRU AMP 0.03252 0.40283 4.79042
22 5D2H AKG 0.0224 0.40088 4.79042
23 3B2Q AES 0.02365 0.40125 4.90405
24 1WS5 MMA 0.008761 0.41583 5.26316
25 1KUJ MMA 0.007014 0.41386 5.26316
26 1UGY GLA BGC 0.01166 0.41186 5.26316
27 1UGY GLA GLC 0.01335 0.40899 5.26316
28 1WS4 AMG 0.01236 0.40833 5.26316
29 1UGW GAL 0.01484 0.40679 5.26316
30 1JAC AMG 0.01416 0.40539 5.26316
31 1WS4 GYP 0.01426 0.40511 5.26316
32 4OYA 1VE 0.03787 0.42989 5.38922
33 3HQP FDP 0.01278 0.40723 5.38922
34 1R27 MGD 0.01259 0.43942 5.98802
35 2J8Z NAP 0.02864 0.41231 5.98802
36 3ZOD HQE 0.02654 0.4115 5.98802
37 2C42 PYR 0.01593 0.42679 6.58683
38 2C42 TPP 0.01593 0.42679 6.58683
39 4JK3 NAD 0.01654 0.42405 6.58683
40 1NV8 MEQ 0.03254 0.40825 6.58683
41 1NV8 SAM 0.03425 0.40825 6.58683
42 5L95 AMP 0.02221 0.40754 6.58683
43 3KRB NAP 0.04596 0.40169 6.58683
44 4M1U MBG A2G 0.03062 0.40414 7.14286
45 1PL6 NAD 0.0146 0.41883 7.18563
46 1VJY 460 0.02587 0.4171 7.18563
47 2C4I BTN 0.01327 0.41355 7.18563
48 1UWK NAD 0.02003 0.43686 7.78443
49 5FA8 SAM 0.03173 0.40325 8.07453
50 3R4S SLB 0.004916 0.42009 8.98204
51 5EFQ ADP 0.01499 0.41206 8.98204
52 4NST ADP 0.01794 0.40769 8.98204
53 3R6U CHT 0.009658 0.42755 10.1796
54 5M67 NAD 0.04819 0.4168 10.7784
55 2PWY SAH 0.01552 0.41966 11.3772
56 4FZV SAM 0.02518 0.40608 11.3772
57 2BOS GLA GAL GLC NBU 0.01018 0.40618 13.2353
58 2BOS GLA GAL GLC 0.01183 0.40195 13.2353
59 2CHT TSA 0.005045 0.4109 13.3858
60 3IT7 TLA 0.01038 0.41393 13.7725
61 1DL5 SAH 0.01797 0.42032 15.5689
62 2BGS NDP 0.03633 0.40935 15.5689
Pocket No.: 2; Query (leader) PDB : 4RDN; Ligand: 6MD; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 4rdn.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UKG MMA 0.002867 0.43584 1.1976
2 1Q8Q MAN MMA 0.0042 0.42759 1.1976
3 2PHU MAN MAN 0.00486 0.42431 1.1976
4 1Q8S MAN MMA 0.005373 0.42166 1.1976
5 2GND MAN 0.005647 0.42047 1.1976
6 2PHT MAN MAN MAN 0.00756 0.41343 1.1976
7 2PHX MAN MAN 0.004454 0.40299 1.1976
8 1Q8O MAN MMA 0.008226 0.40107 1.1976
9 2PHR MAN MAN 0.01222 0.40077 1.1976
10 1Q8V MAN MAN 0.005148 0.40026 1.1976
11 1Y0Y L2O VAL VAL ASP 0.015 0.40384 2.99401
12 1RC0 KT5 0.04219 0.40266 2.99401
13 2RGO FAD 0.04833 0.40662 3.59281
14 4P8K 38C 0.02382 0.43372 4.19162
15 4IJP 1EH 0.02567 0.40166 4.79042
16 5JFL NAD 0.02236 0.41629 5.38922
17 5UAV TFB 0.02878 0.41708 6.58683
18 5UAV NDP 0.02755 0.41708 6.58683
19 2ZJ3 G6P 0.0221 0.40502 7.78443
20 3N7S 3N7 0.008065 0.41166 7.82609
21 3UOY NAP 0.03733 0.43209 8.38323
22 3UOY FAD 0.03733 0.43209 8.38323
23 5FJN FAD 0.04564 0.41238 10.7784
24 1KOJ PAN 0.01173 0.41917 11.3772
25 2NYR SVR 0.005769 0.44475 11.976
26 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.03717 0.40677 13.6842
27 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 0.0181 0.41116 14.3713
28 3ZYR NAG NAG BMA MAN MAN NAG NAG 0.01926 0.40977 14.3713
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