Receptor
PDB id Resolution Class Description Source Keywords
1XMM 2.5 Å EC: 3.-.-.- STRUCTURE OF HUMAN DCPS BOUND TO M7GDP HOMO SAPIENS SCAVENGER DECAPPING ENZYME BOUND M7GDP CHAPERONE
Ref.: CRYSTAL STRUCTURES OF HUMAN DCPS IN LIGAND-FREE AND M7GDP-BOUND FORMS SUGGEST A DYNAMIC MECHANISM FOR S MRNA DECAPPING. J.MOL.BIOL. V. 347 707 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G7M B:1502;
C:503;
 Valid;
Valid;
 none;
none;
 submit data
378.255 C11 H17 N5 O8 P C[n+]...
M7G A:401;
D:404;
 Valid;
Valid;
 none;
none;
 submit data
459.243 C11 H19 N5 O11 P2 CN1CN...
PO4 A:1601;
B:602;
C:603;
D:1604;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ST0 1.9 Å EC: 3.-.-.- STRUCTURE OF DCPS BOUND TO M7GPPPG HOMO SAPIENS RNA DECAY EXOSOME DECAPPING HIT PROTEIN MESSENGER RNA MRNA CAP RNA BINDING PROTEIN
Ref.: INSIGHTS INTO THE STRUCTURE, MECHANISM, AND REGULATION OF SCAVENGER MRNA DECAPPING ACTIVITY MOL.CELL V. 14 67 2004
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 1XMM - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
2 1ST4 - GTA C21 H30 N10 O17 P3 C[n+]1cn(c....
3 1ST0 - GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 3BL9 ic50 = 43.94 nM DD2 C21 H23 Cl2 N5 O c1cc(c(c(c....
2 3BL7 ic50 = 7.62 nM DD1 C21 H24 F N5 O c1ccc(c(c1....
3 5OSY ic50 = 0.0447 uM AJQ C21 H30 N10 O15 P3 S3 C[n+]1cn(c....
4 1XMM - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
5 1ST4 - GTA C21 H30 N10 O17 P3 C[n+]1cn(c....
6 1ST0 - GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 3BL9 ic50 = 43.94 nM DD2 C21 H23 Cl2 N5 O c1cc(c(c(c....
2 3BL7 ic50 = 7.62 nM DD1 C21 H24 F N5 O c1ccc(c(c1....
3 5OSY ic50 = 0.0447 uM AJQ C21 H30 N10 O15 P3 S3 C[n+]1cn(c....
4 1XMM - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
5 1ST4 - GTA C21 H30 N10 O17 P3 C[n+]1cn(c....
6 1ST0 - GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: G7M; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 G7M 1 1
2 MGP 0.794872 0.987013
3 6G0 0.78481 0.987013
4 MG7 0.728571 0.871795
5 GTG 0.655914 0.962025
6 GTA 0.652632 0.962025
7 MGQ 0.629214 0.936709
8 GDP 7MG 0.625 0.961538
9 MGV 0.608696 0.891566
10 5GP 0.583333 0.960526
11 G 0.583333 0.960526
12 AJQ 0.5 0.914634
13 QBQ 0.494624 0.935065
14 GDP 0.483871 0.948052
15 AIR 0.481013 0.855263
16 GP3 0.473118 0.924051
17 MGO 0.46875 0.888889
18 GTP 0.46875 0.948052
19 GP2 0.468085 0.9125
20 GNH 0.463158 0.935897
21 G2P 0.459184 0.9125
22 GMV 0.453608 0.924051
23 A 0.453488 0.87013
24 AMP 0.453488 0.87013
25 AMZ 0.452381 0.87013
26 C2R 0.452381 0.858974
27 93A 0.450549 0.793103
28 GAV 0.45 0.9125
29 XMP 0.449438 0.897436
30 GCP 0.44898 0.924051
31 G1R 0.44898 0.935897
32 GSP 0.444444 0.901235
33 9GM 0.444444 0.924051
34 GNP 0.444444 0.924051
35 NIA 0.44186 0.829268
36 IMP 0.43956 0.934211
37 ALF 5GP 0.438776 0.890244
38 RMB 0.438202 0.805195
39 GDP BEF 0.434343 0.935897
40 6MZ 0.433333 0.883117
41 GPG 0.432692 0.9125
42 RBZ 0.431818 0.807692
43 GTP MG 0.43 0.960526
44 Y9Z 0.429907 0.880952
45 71V 0.428571 0.819277
46 PMO 0.428571 0.807692
47 G2R 0.423077 0.9125
48 IMO 0.422222 0.833333
49 AAM 0.422222 0.87013
50 7RA 0.422222 0.883117
51 YGP 0.420561 0.902439
52 1RB 0.420455 0.792208
53 GKE 0.416667 0.9125
54 GDC 0.416667 0.9125
55 GDD 0.416667 0.9125
56 GDP ALF 0.413462 0.890244
57 GDP AF3 0.413462 0.890244
58 GDR 0.412844 0.936709
59 GFB 0.412844 0.936709
60 IRN 0.4125 0.776316
61 G3A 0.409091 0.924051
62 FAI 0.406593 0.87013
63 G5P 0.405405 0.924051
64 KB7 0.40404 0.829268
65 JB2 0.401786 0.936709
66 GKD 0.401786 0.9125
67 NGD 0.401709 0.936709
68 5O8 0.4 0.729167
Ligand no: 2; Ligand: M7G; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 M7G 1 1
2 MGT 0.910256 1
3 M7M 0.541667 0.963855
4 G8D 0.537634 0.914634
5 TPG 0.525 0.920455
6 8GT 0.494845 0.914634
7 CDP 0.43617 0.829268
8 UDP 0.430108 0.780488
9 M7G A2M G 0.42953 0.88764
10 8GM 0.412371 0.902439
11 8OD 0.411765 0.77907
12 8GD 0.407767 0.872093
Similar Ligands (3D)
Ligand no: 1; Ligand: G7M; Similar ligands found: 48
No: Ligand Similarity coefficient
1 DG 0.9564
2 6OG 0.9468
3 IMU 0.9449
4 DGP 0.9411
5 EO7 0.9400
6 8OG 0.9368
7 FMP 0.9360
8 6CG 0.9332
9 6MA 0.9295
10 DA 0.9294
11 8BR 0.9289
12 LMS 0.9269
13 8GM 0.9268
14 D5M 0.9240
15 8OP 0.9230
16 AOC 0.9200
17 45A 0.9171
18 ABM 0.9165
19 JLN 0.9118
20 7D5 0.9109
21 TMP 0.9109
22 SRA 0.9107
23 NMN 0.9103
24 CNU 0.9102
25 AMP MG 0.9071
26 AS 0.9058
27 IRP 0.9045
28 MTA 0.9045
29 5BU 0.9018
30 A3N 0.8981
31 DI 0.8977
32 NEC 0.8974
33 N5O 0.8972
34 M7G 0.8950
35 FNU 0.8946
36 ZAS 0.8933
37 J7C 0.8907
38 5FU 0.8897
39 6RE 0.8886
40 3DH 0.8785
41 TKW 0.8779
42 PFU 0.8774
43 3F5 0.8766
44 ADP 0.8734
45 NCN 0.8718
46 5HM 0.8661
47 RVP 0.8626
48 TO1 0.8598
Ligand no: 2; Ligand: M7G; Similar ligands found: 55
No: Ligand Similarity coefficient
1 ADP 0.9527
2 GDP 0.9411
3 ADP MG 0.9264
4 7DD 0.9218
5 DAT 0.9211
6 MGO 0.9132
7 DGI 0.9119
8 AP2 0.9114
9 KG4 0.9110
10 GDP BEF 0.9094
11 GDP MG 0.9094
12 MGP 0.9078
13 AN2 0.9051
14 TYD 0.9023
15 A12 0.9022
16 GP2 0.9019
17 M33 0.8967
18 ADX 0.8959
19 G7M 0.8950
20 IDP 0.8945
21 O02 0.8923
22 CA0 0.8922
23 GNH 0.8921
24 CUU 0.8884
25 G 0.8859
26 5GP 0.8859
27 PRX 0.8856
28 KB7 0.8844
29 XMP 0.8832
30 SAH 0.8830
31 GAP 0.8824
32 WSA 0.8810
33 A5A 0.8810
34 ATP 0.8804
35 GJV 0.8789
36 ANP 0.8756
37 SAM 0.8755
38 9ZD 0.8740
39 IMU 0.8738
40 AMP 0.8735
41 5AS 0.8718
42 IMP 0.8716
43 7D3 0.8710
44 2A5 0.8698
45 DGP 0.8681
46 ADP AF3 0.8679
47 AU1 0.8668
48 DG 0.8667
49 GPX 0.8658
50 6CG 0.8638
51 6AD 0.8632
52 EEM 0.8588
53 AGS 0.8576
54 8DG 0.8565
55 ACP 0.8562
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ST0; Ligand: GTG; 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: 1st0.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1ST0; Ligand: GTG; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 1st0.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5BV3 M7G 48.6647
2 5BV3 M7G 48.6647
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