Receptor
PDB id Resolution Class Description Source Keywords
3LUH 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MID DOMAIN FROM HAGO2 IN COMPLEX WITH G HOMO SAPIENS MID DOMAIN RIBONUCLEOPROTEIN RNA-BINDING RNA-MEDIATED GENSILENCING TRANSLATION REGULATION RNA BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR 5'-NUCLEOTIDE BASE-SPECIFIC RECOGNITION OF GUIDE RNA BY HUMAN AGO2. NATURE V. 465 818 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:3;
B:1;
B:4;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 3.3 mM
363.221 C10 H14 N5 O8 P c1nc2...
PO4 C:2;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
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: 5GP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 AN2 0.4 0.894737
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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