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
3QX9 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MID DOMAIN FROM HAGO2 IN COMPLEX WITH A HOMO SAPIENS ROSSMANN-LIKE FOLD RNA BINDING PROTEIN
Ref.: STRUCTURAL ANALYSIS OF 5'-MRNA-CAP INTERACTIONS WIT HUMAN AGO2 MID DOMAIN. EMBO REP. V. 12 415 2011
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 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 3LUJ Kd = 0.12 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 3QX8 Kd = 1.37 mM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
5 3LUG Kd = 3.6 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
6 3QX9 Kd = 0.09 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 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 3LUJ Kd = 0.12 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 3QX8 Kd = 1.37 mM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
5 3LUG Kd = 3.6 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
6 3QX9 Kd = 0.09 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 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 3LUJ Kd = 0.12 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 3QX8 Kd = 1.37 mM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
5 3LUG Kd = 3.6 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
6 3QX9 Kd = 0.09 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 4G0Q Kd = 3 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
8 4G0Y Kd = 4.99 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 4G0P Kd = 0.98 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
10 4G0Z Kd = 6.13 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GTG; Similar ligands found: 104
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 GNP 0.683673 0.91358
14 G3A 0.669811 0.962025
15 G2R 0.666667 0.902439
16 G 0.666667 0.924051
17 5GP 0.666667 0.924051
18 G5P 0.663551 0.962025
19 GMV 0.663265 0.91358
20 G7M 0.655914 0.962025
21 Y9Z 0.650943 0.872093
22 GFB 0.64486 0.95
23 GDR 0.64486 0.95
24 GAV 0.637255 0.902439
25 GDC 0.635514 0.925926
26 GKE 0.635514 0.925926
27 GDD 0.635514 0.925926
28 GP2 0.632653 0.902439
29 GKD 0.627273 0.925926
30 JB2 0.627273 0.95
31 6CK 0.623853 0.903614
32 GPD 0.621622 0.915663
33 GDP MG 0.62 0.890244
34 G2P 0.617647 0.902439
35 NGD 0.617391 0.974684
36 GDP BEF 0.613861 0.869048
37 GPG 0.613208 0.95
38 YGP 0.611111 0.892857
39 GDX 0.607143 0.9375
40 GCP G 0.605769 0.901235
41 CAG 0.6 0.917647
42 ALF 5GP 0.598039 0.858824
43 GTP MG 0.596154 0.890244
44 BEF GDP 0.596154 0.858824
45 JB3 0.594828 0.938272
46 GDP AF3 0.579439 0.858824
47 GDP ALF 0.579439 0.858824
48 TPG 0.571429 0.855556
49 0O2 0.568807 0.924051
50 2MD 0.561983 0.862069
51 FEG 0.55 0.894118
52 G G 0.54955 0.949367
53 MGD 0.548387 0.862069
54 GMP 0.548387 0.825
55 ZGP 0.545455 0.883721
56 MD1 0.543307 0.862069
57 G3D 0.542056 0.924051
58 CG2 0.540984 0.903614
59 MG7 0.537634 0.8625
60 U2G 0.53719 0.903614
61 G4P 0.53211 0.924051
62 PGD 0.53125 0.892857
63 G1G 0.527559 0.9875
64 DBG 0.523077 0.938272
65 GH3 0.522936 0.9125
66 FE9 0.511628 0.791667
67 DGT 0.504587 0.86747
68 3GP 0.5 0.8875
69 G4M 0.496403 0.895349
70 I2C FE2 CMO CMO 0.496124 0.824176
71 GPX 0.486726 0.8875
72 BGO 0.47619 0.9625
73 2GP 0.471154 0.9
74 U A G G 0.469231 0.949367
75 MGO 0.468468 0.879518
76 DGI 0.46789 0.86747
77 G1R G1R 0.466667 0.938272
78 GGM 0.465116 0.939024
79 IDP 0.462963 0.911392
80 G A A A 0.461538 0.9375
81 PGD O 0.452555 0.844444
82 G G U 0.443548 0.949367
83 MGQ 0.439655 0.95
84 P2G 0.435185 0.829268
85 BA3 0.433962 0.886076
86 GPC 0.432836 0.850575
87 B4P 0.429907 0.886076
88 AP5 0.429907 0.886076
89 MGV 0.428571 0.904762
90 P1G 0.427273 0.819277
91 DGP 0.425926 0.855422
92 DG 0.425926 0.855422
93 G C 0.421053 0.891566
94 G2Q 0.420168 0.902439
95 IMP 0.416667 0.898734
96 01G 0.414634 0.872093
97 5FA 0.414414 0.886076
98 AQP 0.414414 0.886076
99 A4P 0.412214 0.862069
100 ATP 0.405405 0.886076
101 G G G C 0.402878 0.926829
102 A2D 0.401869 0.886076
103 G G G RPC 0.4 0.890244
104 U G A 0.4 0.903614
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QX9; Ligand: ATP; Similar sites found: 6
This union binding pocket(no: 1) in the query (biounit: 3qx9.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1L6O SER LEU LYS LEU MET THR THR VAL 0.006847 0.42527 None
2 3SJK LYS PRO VAL LEU ARG THR ALA 0.008008 0.41476 1.57895
3 3ATY FMN 0.0218 0.41155 3.62319
4 2GJP BGC GLC DAF GLC GLC GLC DAF 0.02027 0.44258 4.34783
5 3AI7 TPP 0.03062 0.40514 6.52174
6 4CYI ATP 0.0119 0.42056 13.7681
Pocket No.: 2; Query (leader) PDB : 3QX9; Ligand: ATP; Similar sites found: 57
This union binding pocket(no: 2) in the query (biounit: 3qx9.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1I0S NAP 0.0008809 0.49175 None
2 1I0S FMN 0.0007168 0.48808 None
3 1XSE NDP 0.008569 0.45277 None
4 1QKQ MAN 0.004214 0.44455 None
5 4JB1 FAD 0.04725 0.41904 None
6 4JB1 NAP 0.04909 0.41741 None
7 3K87 FAD 0.003729 0.4647 2.17391
8 4F07 FAD 0.005411 0.43979 2.89855
9 4HVA 4HV 0.01248 0.43122 2.89855
10 4MFL MFK 0.01843 0.43046 2.89855
11 1UP7 NAD 0.01393 0.425 2.89855
12 5IH9 6BF 0.03927 0.41177 2.89855
13 4OSP NAP 0.03791 0.40374 2.89855
14 2CSN CKI 0.0373 0.40157 2.89855
15 3ZOD HQE 0.002107 0.47041 3.62319
16 3TO7 COA 0.03878 0.40094 3.62319
17 3AFH GSU 0.005102 0.437 4.34783
18 1PVC ILE SER GLU VAL 0.00005132 0.43066 4.34783
19 3MJE NDP 0.01657 0.42489 4.34783
20 5IXJ THR 0.04109 0.4122 4.34783
21 5FUI APY 0.01277 0.40369 4.54545
22 2GOU FMN 0.008219 0.44558 5.07246
23 2WD7 NAP 0.01432 0.42764 5.07246
24 5K6A NAP 0.01632 0.42578 5.07246
25 3JQ9 NAP 0.01749 0.42377 5.07246
26 5JDI NAP 0.01751 0.42282 5.07246
27 3CV6 HXS 0.04106 0.41404 5.07246
28 3CV6 NAP 0.04364 0.41173 5.07246
29 3JQA DX4 0.0234 0.40498 5.07246
30 2JAH NDP 0.04245 0.40367 5.07246
31 1KQB FMN 0.03343 0.40107 5.07246
32 1OJZ NAD 0.01619 0.40884 5.7971
33 1WLE SRP 0.02704 0.40079 5.7971
34 4LJ3 C2E 0.006705 0.43886 6.52174
35 1XKQ NDP 0.04897 0.40268 6.52174
36 3A5Z KAA 0.006476 0.44331 7.24638
37 1MXH NAP 0.02791 0.42168 7.24638
38 4O1M NAD 0.03596 0.4073 7.24638
39 3I7V B4P 0.0001357 0.54637 7.46269
40 2RCU BUJ 0.03137 0.43058 7.97101
41 4PVD NDP 0.01902 0.41817 7.97101
42 3HF3 FMN 0.03453 0.40102 8.69565
43 3UEC ALA ARG TPO LYS 0.001611 0.45706 10.1449
44 4MFZ MFK 0.008709 0.4388 10.1449
45 1R6U TYM 0.02037 0.41515 10.1449
46 1X54 4AD 0.01666 0.4193 10.8696
47 1YQS BSA 0.02696 0.41848 10.8696
48 3H4V NAP 0.032 0.40888 10.8696
49 2V6G NAP 0.04399 0.40382 10.8696
50 3PJU C2E 0.009363 0.43521 13.0435
51 4KQR VPP 0.01691 0.41103 13.0435
52 4XP7 FNR 0.02215 0.4067 13.0435
53 3QWI NAP 0.04261 0.40539 13.0435
54 5F3I 5UJ 0.04558 0.42052 15.2174
55 2D37 FMN 0.01721 0.42146 16.6667
56 2D37 NAD 0.0182 0.42146 16.6667
57 3PTG 932 0.009157 0.41403 21.0145
Pocket No.: 3; Query (leader) PDB : 3QX9; Ligand: ATP; Similar sites found: 19
This union binding pocket(no: 3) in the query (biounit: 3qx9.bio3) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.0105 0.40699 None
2 2FAV APR 0.03186 0.40546 1.44928
3 1SVK ALF GDP 0.02782 0.41257 2.17391
4 3E9I XAH 0.03153 0.41059 2.89855
5 3CH6 311 0.03877 0.42447 3.62319
6 3CH6 NAP 0.03877 0.42447 3.62319
7 4A3U FMN 0.02664 0.40403 3.62319
8 1ICP FMN 0.03714 0.40459 4.34783
9 4C2C ALA ALA ALA 0.0125 0.40318 4.34783
10 4TW7 37K 0.03663 0.40287 4.6875
11 4J75 TYM 0.009467 0.4367 5.7971
12 2JFN UMA 0.01876 0.40229 5.7971
13 4A91 GLU 0.004226 0.42298 6.52174
14 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.04431 0.40284 6.52174
15 3A5Y KAA 0.003338 0.45601 7.24638
16 1MXH DHF 0.02224 0.4274 7.24638
17 1E6E FAD 0.04338 0.40995 7.97101
18 1R37 NAD 0.04133 0.40774 7.97101
19 4OYA 1VE 0.04378 0.42707 21.0145
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