Receptor
PDB id Resolution Class Description Source Keywords
3QX8 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MID DOMAIN FROM HAGO2 IN COMPLEX WITH M HOMO SAPIENS ROSSMANN-LIKE FOLDE RNA BINDING SMALL RNA RNA BINDING PRO
Ref.: STRUCTURAL ANALYSIS OF 5'-MRNA-CAP INTERACTIONS WIT HUMAN AGO2 MID DOMAIN. EMBO REP. V. 12 415 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTG A:28;
B:28;
C:28;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 1.37 mM
803.44 C21 H30 N10 O18 P3 C[n+]...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
7C6B 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF AGO2 MID DOMAIN IN COMPLEX WITH 6-(3-(2 CARBOXYETHYL)PHENYL)PURINE RIBOSIDE MONOPHOSPHATE HOMO SAPIENS ARGONAUTE MID DOMAIN RIBONUCLEOPROTEIN RNA-BINDING RNA-MGENE SILENCING TRANSLATION REGULATION RNA BINDING PROTEIN
Ref.: SIRNA POTENCY ENHANCEMENT VIA CHEMICAL MODIFICATION NUCLEOTIDE BASES AT THE 5'-END OF THE SIRNA GUIDE S RNA 2020
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3LUH Kd = 3.3 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3LUD Kd = 0.26 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 7D7U Kd = 100 uM 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
4 3LUJ Kd = 0.12 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
5 3QX8 Kd = 1.37 mM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
6 7C6B Kd = 42 uM K2R C19 H21 N4 O9 P c1cc(cc(c1....
7 3LUG Kd = 3.6 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
8 3QX9 Kd = 0.09 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3LUH Kd = 3.3 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3LUD Kd = 0.26 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 7D7U Kd = 100 uM 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
4 3LUJ Kd = 0.12 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
5 3QX8 Kd = 1.37 mM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
6 7C6B Kd = 42 uM K2R C19 H21 N4 O9 P c1cc(cc(c1....
7 3LUG Kd = 3.6 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
8 3QX9 Kd = 0.09 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3LUH Kd = 3.3 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3LUD Kd = 0.26 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 7D7U Kd = 100 uM 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
4 3LUJ Kd = 0.12 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
5 3QX8 Kd = 1.37 mM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
6 7C6B Kd = 42 uM K2R C19 H21 N4 O9 P c1cc(cc(c1....
7 3LUG Kd = 3.6 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
8 3QX9 Kd = 0.09 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
9 4G0Q Kd = 3 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
10 4G0Y Kd = 4.99 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
11 4G0P Kd = 0.98 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
12 4G0Z Kd = 6.13 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GTG; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 GTG 1 1
2 GP3 0.806818 0.962025
3 GDP 7MG 0.79798 0.974684
4 6G0 0.752688 0.974684
5 GTP 0.752688 0.936709
6 MGP 0.741935 0.974684
7 GSP 0.736842 0.891566
8 GDP 0.72043 0.936709
9 GNH 0.712766 0.925
10 G1R 0.708333 0.925
11 GCP 0.690722 0.91358
12 GTA 0.688679 1
13 9GM 0.683673 0.91358
14 GNP 0.683673 0.91358
15 G3A 0.669811 0.962025
16 G2R 0.666667 0.902439
17 5GP 0.666667 0.924051
18 G 0.666667 0.924051
19 G5P 0.663551 0.962025
20 GMV 0.663265 0.91358
21 G7M 0.655914 0.962025
22 Y9Z 0.650943 0.872093
23 GFB 0.64486 0.95
24 GDR 0.64486 0.95
25 GAV 0.637255 0.902439
26 GKE 0.635514 0.925926
27 GDD 0.635514 0.925926
28 GDC 0.635514 0.925926
29 GP2 0.632653 0.902439
30 JB2 0.627273 0.95
31 GKD 0.627273 0.925926
32 6CK 0.623853 0.903614
33 GPD 0.621622 0.915663
34 G2P 0.617647 0.902439
35 NGD 0.617391 0.974684
36 GPG 0.613208 0.95
37 YGP 0.611111 0.892857
38 GDP BEF 0.607843 0.901235
39 GDX 0.607143 0.9375
40 GTP MG 0.601942 0.924051
41 CAG 0.6 0.917647
42 ALF 5GP 0.598039 0.858824
43 JB3 0.594828 0.938272
44 GDP AF3 0.579439 0.858824
45 GDP ALF 0.579439 0.858824
46 TPG 0.571429 0.855556
47 0O2 0.568807 0.924051
48 KB7 0.563107 0.8
49 2MD 0.561983 0.862069
50 FEG 0.55 0.894118
51 MGD 0.548387 0.862069
52 GMP 0.548387 0.825
53 ZGP 0.545455 0.883721
54 MD1 0.543307 0.862069
55 G3D 0.542056 0.924051
56 CG2 0.540984 0.903614
57 MG7 0.537634 0.8625
58 U2G 0.53719 0.903614
59 G4P 0.53211 0.924051
60 PGD 0.53125 0.892857
61 G1G 0.527559 0.9875
62 AKW 0.52459 0.951219
63 DBG 0.523077 0.938272
64 GH3 0.522936 0.9125
65 KBD 0.513274 0.821429
66 FE9 0.511628 0.791667
67 QBQ 0.504673 0.924051
68 DGT 0.504587 0.86747
69 3GP 0.5 0.8875
70 G4M 0.496403 0.895349
71 KBJ 0.495726 0.793103
72 I2C FE2 CMO CMO 0.48855 0.824176
73 GPX 0.486726 0.8875
74 BGO 0.47619 0.9625
75 AJQ 0.472441 0.951219
76 2GP 0.471154 0.9
77 MGO 0.468468 0.879518
78 DGI 0.46789 0.86747
79 G1R G1R 0.466667 0.938272
80 GGM 0.465116 0.939024
81 IDP 0.462963 0.911392
82 R5I 0.459459 0.8875
83 R7I 0.459459 0.8875
84 CZF 0.454545 0.875
85 PGD O 0.452555 0.844444
86 MGQ 0.439655 0.95
87 P2G 0.435185 0.829268
88 BA3 0.433962 0.886076
89 GPC 0.432836 0.850575
90 B4P 0.429907 0.886076
91 AP5 0.429907 0.886076
92 MGV 0.428571 0.904762
93 P1G 0.427273 0.819277
94 DG 0.425926 0.855422
95 DGP 0.425926 0.855422
96 G C 0.421053 0.891566
97 G2Q 0.420168 0.902439
98 IMP 0.416667 0.898734
99 01G 0.414634 0.872093
100 AQP 0.414414 0.886076
101 5FA 0.414414 0.886076
102 A4P 0.412214 0.862069
103 HFD 0.40708 0.843373
104 JSQ 0.40708 0.843373
105 HEJ 0.405405 0.886076
106 ATP 0.405405 0.886076
107 A2D 0.401869 0.886076
108 APC G U 0.4 0.901235
Similar Ligands (3D)
Ligand no: 1; Ligand: GTG; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 7C6B; Ligand: K2R; 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: 7c6b.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 7C6B; Ligand: K2R; 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: 7c6b.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 7C6B; Ligand: K2R; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 7c6b.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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