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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 1443 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 1205 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 1039 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: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 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 G1R 0.765432 0.973333
11 GCP 0.765432 0.960526
12 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GMP 0.732394 0.866667
18 GPG 0.724138 0.948052
19 G2R 0.712644 0.948052
20 ALF GDP 0.701149 0.9
21 GDP ALF 0.701149 0.9
22 GDP AF3 0.701149 0.9
23 GKE 0.692308 0.948052
24 Y9Z 0.692308 0.890244
25 GDC 0.692308 0.948052
26 GDD 0.692308 0.948052
27 YGP 0.681319 0.9125
28 G3A 0.677419 0.960526
29 G5P 0.670213 0.960526
30 GFB 0.666667 0.948052
31 GDR 0.666667 0.948052
32 GTG 0.666667 0.924051
33 6CK 0.659574 0.924051
34 3GP 0.65 0.959459
35 G G 0.648936 0.960526
36 GKD 0.645833 0.948052
37 JB2 0.645833 0.948052
38 GDX 0.639175 0.960526
39 GPD 0.639175 0.9125
40 GDP 7MG 0.635417 0.923077
41 G3D 0.617977 0.972973
42 U2G 0.617647 0.924051
43 2GP 0.609756 0.946667
44 IMP 0.609756 0.972603
45 JB3 0.607843 0.935897
46 CG2 0.605769 0.924051
47 G4P 0.604396 0.972973
48 DGP 0.60241 0.922078
49 DG 0.60241 0.922078
50 FEG 0.601942 0.890244
51 NGD 0.601942 0.948052
52 ZGP 0.596154 0.879518
53 0O2 0.595745 0.972973
54 2MD 0.584906 0.879518
55 G7M 0.583333 0.960526
56 CAG 0.583333 0.869048
57 G A A A 0.579439 0.935065
58 A G 0.579439 0.947368
59 U A G G 0.574074 0.947368
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 PGD 0.5625 0.9125
63 MD1 0.5625 0.879518
64 P2G 0.55814 0.894737
65 GCP G 0.556701 0.933333
66 FE9 0.553571 0.784946
67 P1G 0.545455 0.883117
68 GH3 0.542553 0.96
69 TPG 0.53913 0.829545
70 GPX 0.53125 0.933333
71 DGI 0.527473 0.910256
72 G1R G1R 0.525862 0.911392
73 G U 0.522936 0.911392
74 PGD O 0.521368 0.83908
75 DGT 0.521277 0.910256
76 G4M 0.520325 0.869048
77 AKW 0.513761 0.878049
78 G C 0.513514 0.911392
79 93A 0.511364 0.821429
80 IDP 0.505495 0.959459
81 MGQ 0.505155 0.948052
82 C2R 0.5 0.893333
83 A 0.5 0.905405
84 AMZ 0.5 0.905405
85 BGO 0.5 0.911392
86 AMP 0.5 0.905405
87 AIR 0.493671 0.890411
88 MGV 0.49 0.901235
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 G G G RPC 0.473684 0.886076
93 GGM 0.473684 0.888889
94 71V 0.47191 0.85
95 APC G U 0.470085 0.897436
96 R5I 0.46875 0.933333
97 R7I 0.46875 0.933333
98 MGP 0.46875 0.948052
99 35G 0.468085 0.945946
100 PCG 0.468085 0.945946
101 C2E 0.468085 0.933333
102 G1G 0.466102 0.9125
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 FAI 0.465909 0.905405
106 7RA 0.465909 0.918919
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 JLN 0.433333 0.88
124 P2P 0.433333 0.842105
125 A G U U 0.42963 0.9
126 XMP 0.428571 0.907895
127 PGS 0.425532 0.804878
128 RVP 0.423529 0.84
129 G2Q 0.423077 0.948052
130 ADP 0.419355 0.906667
131 ABM 0.417582 0.857143
132 A2D 0.417582 0.881579
133 PRT 0.416667 0.945946
134 GUO 0.415842 0.932432
135 AT4 0.414894 0.871795
136 CA0 0.410526 0.883117
137 2SA 0.41 0.871795
138 1YD 0.409091 0.933333
139 4BW 0.409091 0.933333
140 A12 0.408602 0.871795
141 AP2 0.408602 0.871795
142 BA3 0.408602 0.881579
143 6C6 0.408163 0.825
144 25A 0.407767 0.906667
145 NOS 0.406977 0.813333
146 HEJ 0.40625 0.906667
147 ATP 0.40625 0.906667
148 AP5 0.404255 0.881579
149 B4P 0.404255 0.881579
150 ACQ 0.40404 0.883117
151 6IA 0.40404 0.785714
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 APC 0.402062 0.871795
155 3ZE 0.402062 0.871795
156 5FA 0.402062 0.906667
157 AQP 0.402062 0.906667
158 N6P 0.4 0.853333
159 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 with APoc: 18
This union binding pocket(no: 1) in the query (biounit: 3qx9.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1L6O SER LEU LYS LEU MET THR THR VAL None
2 2ZFZ ARG None
3 3SJK LYS PRO VAL LEU ARG THR ALA 1.57895
4 5UBG PRT 2.89855
5 3ATY FMN 3.62319
6 1RKX NAD 4.34783
7 4KWI 1TJ 5.7971
8 4KWI NAP 5.7971
9 2BD0 NAP 5.7971
10 2FXU BID 6.52174
11 3AI7 TPP 6.52174
12 1EB1 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 7.24638
13 5TA6 79D 8.69565
14 2BEK ATP 8.94942
15 2IVD FAD 9.42029
16 3RMK BML 11.5942
17 4CYI ATP 13.7681
18 3O84 HTJ 17.3913
Pocket No.: 2; Query (leader) PDB : 3QX9; Ligand: ATP; Similar sites found with APoc: 163
This union binding pocket(no: 2) in the query (biounit: 3qx9.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1I0S NAP None
2 1I0S FMN None
3 1XSE NDP None
4 3HV8 C2E None
5 1USF NAP None
6 1USF FMN None
7 5ZEC NAP None
8 5VKM GAL SIA None
9 4JB1 FAD None
10 4JB1 NAP None
11 1S8F GDP None
12 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU None
13 1YNQ NDP None
14 5ANU 58T None
15 5CG1 NAD BBN None
16 4YC0 5OF None
17 1GZ6 NAI None
18 3K87 FAD 2.17391
19 4MSG 2C6 2.17391
20 3QBT GNP 2.17391
21 3KJD 78P 2.17391
22 4L9Z OXL 2.17391
23 4L9Z COA 2.17391
24 3WR7 COA 2.17391
25 5Z2L NDP 2.17391
26 1FK8 NAD 2.17391
27 1Y1P NMN AMP PO4 2.17391
28 4F07 FAD 2.89855
29 4HVA 4HV 2.89855
30 4MFL MFK 2.89855
31 1UP7 NAD 2.89855
32 5WUW NAP 2.89855
33 4L6C 0BT 2.89855
34 5W11 CTR 2.89855
35 4OSP NAP 2.89855
36 2CSN CKI 2.89855
37 3E9I XAH 2.89855
38 3ZOD HQE 3.62319
39 3ZOD FMN 3.62319
40 6H3O FAD 3.62319
41 3H7R NAP 3.62319
42 1LLU NAD 3.62319
43 5EH0 5NW 3.62319
44 4O0L NDP 3.62319
45 2ZBA COA 3.62319
46 3HMO STU 3.62319
47 3TO7 COA 3.62319
48 1PVC ILE SER GLU VAL 4.34783
49 3AFH GSU 4.34783
50 3WB0 FEG 4.34783
51 2Z3U CRR 4.34783
52 5GT9 NAP 4.34783
53 1JIL 485 4.34783
54 2FGE ALA ALA LEU THR ARG ALA 4.34783
55 6BMN PAP 4.34783
56 5FUI APY 4.54545
57 2GOU FMN 5.07246
58 4CM9 NAP 5.07246
59 5JDC NAP 5.07246
60 5JDI NAP 5.07246
61 5JCJ NAP 5.07246
62 2WD7 NAP 5.07246
63 2VZ0 NAP 5.07246
64 2VZ0 D64 5.07246
65 3BMQ NAP 5.07246
66 4CMI NAP 5.07246
67 4CM8 NAP 5.07246
68 5K6A NAP 5.07246
69 4CM4 NAP 5.07246
70 4CLR NAP 5.07246
71 2PVN P63 5.07246
72 4CME NAP 5.07246
73 3BMN NAP 5.07246
74 3CV6 HXS 5.07246
75 3JQ7 NAP 5.07246
76 4CLO NAP 5.07246
77 3CV6 NAP 5.07246
78 3BMO NAP 5.07246
79 3JQF NAP 5.07246
80 3JQG NAP 5.07246
81 6MPT C30 5.07246
82 3JQ9 NAP 5.07246
83 3JQB NAP 5.07246
84 3JQ8 NAP 5.07246
85 2R14 TXD 5.07246
86 3JQA NAP 5.07246
87 3JQA DX4 5.07246
88 2R14 FMN 5.07246
89 2JAH NDP 5.07246
90 1KQB FMN 5.07246
91 5MF5 C2E 5.7971
92 5DK4 5BX 5.7971
93 4J75 TYM 5.7971
94 5DK4 ATP 5.7971
95 1OJZ NAD 5.7971
96 1HFU NAG NDG 5.7971
97 5YEC ATP 5.7971
98 1WLE SRP 5.7971
99 2DKN NAI 5.7971
100 4U03 TLL 6.52174
101 4U03 GTP 6.52174
102 4LJ3 C2E 6.52174
103 3SBZ MLI 6.52174
104 2UUU FAD 6.52174
105 2B4Q NAP 6.52174
106 6CI9 NAP 6.52174
107 2ZTG A5A 6.52174
108 1XKQ NDP 6.52174
109 3A5Z KAA 7.24638
110 1MXH NAP 7.24638
111 4JIQ FMN 7.24638
112 4JIQ 1L5 7.24638
113 4R57 ACO 7.24638
114 4O1M NAD 7.24638
115 5T79 NDP 7.24638
116 3I7V B4P 7.46269
117 2RCU BUJ 7.97101
118 4PVD NDP 7.97101
119 1R37 NAD 7.97101
120 3GEG NAD 7.97101
121 1E8G FAD 8.69565
122 1E8G FCR 8.69565
123 1T36 ADP 8.69565
124 3HF3 FMN 8.69565
125 5N5U 7N8 9.42029
126 5OGX FAD 9.42029
127 3SJU NDP 9.42029
128 4H8N NDP 9.42029
129 6H45 QEI 9.42029
130 1RPN NDP 9.42029
131 3UEC ALA ARG TPO LYS 10.1449
132 4MFZ MFK 10.1449
133 1R6U TYM 10.1449
134 4CQM NAP 10.1449
135 1X54 4AD 10.8696
136 1YQS BSA 10.8696
137 3H4V DVP 10.8696
138 3H4V NAP 10.8696
139 4NVQ 2OD 10.8696
140 2V6G NAP 10.8696
141 4NVQ SAH 10.8696
142 1VYP FMN 10.8696
143 3F8D FAD 11.5942
144 3DEK RXD 11.5942
145 5YSS NAD 12.3188
146 2D3Y DU 12.3188
147 4YRY FAD 12.3188
148 6A1G 9OL 12.3188
149 3PJU C2E 13.0435
150 4KQR VPP 13.0435
151 3AL3 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 13.0435
152 3QWI NAP 13.0435
153 4FN4 NAD 14.4928
154 5F3I 5UJ 15.2174
155 6FX2 FUC C4W NAG BMA MAN NAG GAL 16.2791
156 2D37 FMN 16.6667
157 2D37 NAD 16.6667
158 1XL8 OCB 18.8406
159 4QVB F42 18.8406
160 2II3 CAO 18.8406
161 1XK9 P34 18.8406
162 3PTG 932 21.0145
163 4G6I RS3 22.4638
Pocket No.: 3; Query (leader) PDB : 3QX9; Ligand: ATP; Similar sites found with APoc: 53
This union binding pocket(no: 3) in the query (biounit: 3qx9.bio3) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1QKQ MAN None
2 4KOT CE3 None
3 1R1Q ACE ARG GLU PTR VAL ASN VAL None
4 2FAV APR 1.44928
5 1SVK ALF GDP 2.17391
6 1FLM FMN 3.27869
7 3CH6 311 3.62319
8 3CH6 NAP 3.62319
9 4A3U FMN 3.62319
10 3TN7 NJP 3.89105
11 5XWV NDP 4.34783
12 1ICP FMN 4.34783
13 4C2C ALA ALA ALA 4.34783
14 4L80 1VU 4.34783
15 1W8D NAP 4.34783
16 4TW7 37K 4.6875
17 1JYQ MAZ PTR PTM ASN 5.20833
18 1DJL NAP 5.7971
19 5MKG C2E 5.7971
20 2JFN UMA 5.7971
21 5LYH 7B8 6.52174
22 4A91 GLU 6.52174
23 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 6.52174
24 3A5Y KAA 7.24638
25 1MXH DHF 7.24638
26 2PID YSA 7.24638
27 5ZCM NDP DTT 7.24638
28 4KXL 6C6 7.97101
29 1E6E FAD 7.97101
30 5BVE 4VG 8.69565
31 2CYB TYR 8.69565
32 2WZM NA7 8.69565
33 1NU4 MLA 9.27835
34 5N5U AMP 9.42029
35 4PJT 2YQ 9.42029
36 2FY3 CHT 10.1449
37 1R6T TYM 11.5942
38 5JCA FAD 11.5942
39 6DWD GTP 12.3188
40 6DWD HDV 12.3188
41 4CS4 AXZ 12.3188
42 2JLD AG1 13.0435
43 5M1T C2E 13.7681
44 1EP2 FAD 13.7681
45 5J62 FMN 14.4928
46 3ZLQ 6T9 14.7541
47 3IAL PR8 15.942
48 2HSA FMN 17.3913
49 2BVD ISX 18.8406
50 4OYA 1VE 21.0145
51 5GK9 ACO 22
52 6B92 SAH 22.4638
53 5V59 8X1 26.8116
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