Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K2R B:601;
C:601;
A:601;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 42 uM
480.365 C19 H21 N4 O9 P c1cc(...
PO4 C:602;
C:603;
Invalid;
Invalid;
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
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: K2R; Similar ligands found: 97
No: Ligand ECFP6 Tc MDL keys Tc
1 K2R 1 1
2 N6P 0.63 0.929577
3 AMP 0.510638 0.878378
4 A 0.510638 0.878378
5 2SA 0.509615 0.92
6 6MZ 0.505155 0.866667
7 IMO 0.494845 0.916667
8 ERJ 0.479167 0.746667
9 6K6 0.477064 0.866667
10 6C6 0.466667 0.87013
11 6IA 0.462264 0.82716
12 V2G 0.457944 0.884615
13 ITT 0.456311 0.90411
14 KG4 0.451923 0.881579
15 HEJ 0.451923 0.88
16 ATP 0.451923 0.88
17 ADP 0.45098 0.88
18 5FA 0.447619 0.88
19 AQP 0.447619 0.88
20 WAQ 0.447368 0.896104
21 PGS 0.442308 0.825
22 CA0 0.442308 0.881579
23 71V 0.441176 0.802469
24 B4P 0.436893 0.88
25 AP5 0.436893 0.88
26 A2D 0.435644 0.88
27 ABM 0.435644 0.831169
28 45A 0.435644 0.831169
29 T99 0.435185 0.846154
30 TAT 0.435185 0.846154
31 APC 0.433962 0.87013
32 C2R 0.43299 0.842105
33 AT4 0.432692 0.846154
34 AMP MG 0.43 0.84
35 DLL 0.429825 0.918919
36 BA3 0.427184 0.88
37 A12 0.427184 0.87013
38 AP2 0.427184 0.87013
39 3UK 0.426087 0.906667
40 25A 0.424779 0.905405
41 OOB 0.424779 0.918919
42 6YZ 0.423423 0.881579
43 PR8 0.422414 0.8625
44 B5V 0.422414 0.894737
45 ACQ 0.422018 0.881579
46 RMB 0.421569 0.861111
47 AMO 0.421053 0.894737
48 B5M 0.420168 0.883117
49 NO7 0.419643 0.846154
50 KOY 0.419355 0.815789
51 SON 0.419048 0.92
52 AN2 0.419048 0.868421
53 AMZ 0.418367 0.828947
54 5AL 0.418182 0.893333
55 8LE 0.418182 0.858974
56 7MD 0.418033 0.851852
57 8LQ 0.415929 0.894737
58 SRA 0.415842 0.833333
59 M33 0.415094 0.844156
60 ADX 0.415094 0.77381
61 AU1 0.415094 0.857143
62 8QN 0.412281 0.893333
63 9SN 0.411765 0.860759
64 50T 0.411215 0.844156
65 ACP 0.411215 0.881579
66 8LH 0.410714 0.87013
67 SRP 0.410714 0.894737
68 NIA 0.41 0.746988
69 GAP 0.409091 0.857143
70 ANP 0.409091 0.857143
71 PAJ 0.408696 0.82716
72 FA5 0.408333 0.92
73 B5Y 0.408333 0.883117
74 JLN 0.407767 0.853333
75 APR 0.407407 0.88
76 AR6 0.407407 0.88
77 PRX 0.407407 0.833333
78 1ZZ 0.40678 0.829268
79 TXA 0.40678 0.87013
80 PTJ 0.40678 0.860759
81 FYA 0.40678 0.868421
82 1RB 0.405941 0.873239
83 ADP BEF 0.40566 0.853333
84 ADP MG 0.40566 0.853333
85 AHX 0.405172 0.8375
86 00A 0.405172 0.871795
87 ARU 0.405172 0.804878
88 RBY 0.40367 0.87013
89 ADV 0.40367 0.87013
90 AGS 0.40367 0.835443
91 AD9 0.40367 0.857143
92 QA7 0.403509 0.858974
93 DQV 0.403226 0.893333
94 RBZ 0.401961 0.837838
95 PMO 0.4 0.837838
96 9ZD 0.4 0.871795
97 9ZA 0.4 0.871795
Similar Ligands (3D)
Ligand no: 1; Ligand: K2R; 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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