Receptor
PDB id Resolution Class Description Source Keywords
7D7U 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF AGO2 MID DOMAIN IN COMPLEX WITH 8-BR-AD 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8BR A:601;
C:601;
B:601;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 100 uM
426.117 C10 H13 Br N5 O7 P c1nc(...
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: 8BR; Similar ligands found: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 8BR 1 1
2 5NB 0.676471 0.842105
3 Z8B 0.582278 0.8125
4 5CI 0.54023 0.792683
5 A 0.525 0.931507
6 AMP 0.525 0.931507
7 3BH 0.466667 0.802632
8 C2R 0.451219 0.844156
9 7D5 0.451219 0.844156
10 3F5 0.444444 0.775
11 A12 0.443182 0.871795
12 AP2 0.443182 0.871795
13 HEJ 0.43956 0.906667
14 ATP 0.43956 0.906667
15 ADP 0.438202 0.906667
16 45A 0.436782 0.881579
17 ABM 0.436782 0.881579
18 A2D 0.436782 0.881579
19 AAM 0.436782 0.931507
20 AQP 0.434783 0.906667
21 5FA 0.434783 0.906667
22 APC 0.434783 0.871795
23 NBP 0.434426 0.948052
24 AMZ 0.433735 0.855263
25 ZNB 0.431193 0.714286
26 AMP MG 0.430233 0.891892
27 CA0 0.428571 0.858974
28 ADX 0.428571 0.797619
29 A2P 0.426966 0.891892
30 71V 0.426966 0.85
31 BA3 0.426966 0.881579
32 RVP 0.426829 0.792208
33 AIR 0.425 0.890411
34 25A 0.424242 0.906667
35 KG4 0.423913 0.858974
36 NIA 0.423529 0.792683
37 AP5 0.422222 0.881579
38 B4P 0.422222 0.881579
39 T99 0.421053 0.871795
40 TAT 0.421053 0.871795
41 AN2 0.417582 0.894737
42 AT4 0.417582 0.871795
43 N8M 0.416667 0.7375
44 6MZ 0.41573 0.893333
45 RBY 0.414894 0.848101
46 ADV 0.414894 0.848101
47 SRA 0.413793 0.883117
48 M33 0.413043 0.87013
49 AU1 0.413043 0.883117
50 A3P 0.411111 0.905405
51 50T 0.408602 0.894737
52 ACP 0.408602 0.883117
53 8ID 0.40708 0.898734
54 V3L 0.40625 0.906667
55 ACQ 0.40625 0.883117
56 GAP 0.40625 0.835443
57 IMO 0.404494 0.866667
58 7RA 0.404494 0.918919
59 AR6 0.404255 0.881579
60 PRX 0.404255 0.858974
61 APR 0.404255 0.881579
62 ADP MG 0.402174 0.88
63 ADP BEF 0.402174 0.88
64 V2G 0.402062 0.839506
65 APC MG 0.4 0.857143
66 AD9 0.4 0.883117
67 AGS 0.4 0.860759
Similar Ligands (3D)
Ligand no: 1; Ligand: 8BR; Similar ligands found: 109
No: Ligand Similarity coefficient
1 8OP 0.9659
2 5GP 0.9643
3 IMP 0.9570
4 G 0.9516
5 IRP 0.9482
6 8GM 0.9401
7 XMP 0.9376
8 U5P 0.9372
9 DG 0.9361
10 DGP 0.9361
11 6CG 0.9334
12 C 0.9334
13 C5P 0.9326
14 TMP 0.9313
15 FMP 0.9296
16 D5M 0.9294
17 AOC 0.9291
18 6OG 0.9291
19 G7M 0.9289
20 TKW 0.9281
21 5BU 0.9279
22 CH 0.9257
23 BRU 0.9254
24 5CM 0.9253
25 8OG 0.9250
26 UP6 0.9249
27 N5O 0.9243
28 PSU 0.9241
29 ZAS 0.9238
30 O8M 0.9237
31 NCN 0.9229
32 UFP 0.9228
33 BMP 0.9224
34 DA 0.9216
35 NEC 0.9214
36 UMP 0.9207
37 BMQ 0.9207
38 5AS 0.9176
39 5FU 0.9172
40 5HM 0.9160
41 H2U 0.9146
42 FN5 0.9133
43 6MA 0.9124
44 CMP 0.9121
45 2DT 0.9111
46 D4M 0.9110
47 U 0.9103
48 QBT 0.9101
49 DCM 0.9086
50 FAI 0.9084
51 NUP 0.9078
52 S5P 0.9077
53 JLN 0.9068
54 MTH 0.9067
55 A3N 0.9067
56 NYM 0.9054
57 MTE 0.9048
58 5HU 0.9046
59 MTA 0.9018
60 DC 0.9006
61 6CN 0.9004
62 FDM 0.8996
63 DUS 0.8983
64 SP1 0.8977
65 5IU 0.8974
66 JW5 0.8966
67 OMP 0.8966
68 KB7 0.8966
69 DU 0.8959
70 FNU 0.8958
71 T3S 0.8945
72 MTM 0.8942
73 U2S 0.8941
74 U6M 0.8939
75 EP4 0.8937
76 U4S 0.8933
77 MTI 0.8931
78 U1S 0.8921
79 U3S 0.8921
80 NWQ 0.8905
81 NMN 0.8900
82 16B 0.8880
83 PFU 0.8872
84 UMC 0.8870
85 9L3 0.8862
86 DOC 0.8853
87 6J7 0.8839
88 6AU 0.8835
89 CAR 0.8834
90 A8M 0.8826
91 DDN 0.8787
92 0NH 0.8774
93 SU1 0.8761
94 43J 0.8757
95 ADN 0.8751
96 E3Y 0.8743
97 DSH 0.8739
98 HDU 0.8731
99 8OD 0.8727
100 MZP 0.8725
101 E44 0.8717
102 IXF 0.8677
103 TAL 0.8669
104 BVP 0.8647
105 S4M 0.8645
106 NOS 0.8629
107 O7M 0.8591
108 2OM 0.8556
109 DN8 0.8519
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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