Receptor
PDB id Resolution Class Description Source Keywords
4G0P 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN WITH UMP ARABIDOPSIS THALIANA MID DOMAIN SMALL RNA 5-prime NUCLEOTIDE RECOGNITION GENE REGULA
Ref.: ARABIDOPSIS ARGONAUTE MID DOMAINS USE THEIR NUCLEOT SPECIFICITY LOOP TO SORT SMALL RNAS. EMBO J. V. 31 3588 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U5P A:801;
Valid;
none;
Kd = 0.98 mM
324.181 C9 H13 N2 O9 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4G0P 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN WITH UMP ARABIDOPSIS THALIANA MID DOMAIN SMALL RNA 5-prime NUCLEOTIDE RECOGNITION GENE REGULA
Ref.: ARABIDOPSIS ARGONAUTE MID DOMAINS USE THEIR NUCLEOT SPECIFICITY LOOP TO SORT SMALL RNAS. EMBO J. V. 31 3588 2012
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4G0Q Kd = 3 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 4G0Y Kd = 4.99 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 4G0P Kd = 0.98 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4G0Z Kd = 6.13 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4G0Q Kd = 3 mM C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 4G0Y Kd = 4.99 mM AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 4G0P Kd = 0.98 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4G0Z Kd = 6.13 mM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
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: U5P; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4G0P; Ligand: U5P; Similar sites found: 30
This union binding pocket(no: 1) in the query (biounit: 4g0p.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1I0S FMN 0.002638 0.4574 None
2 1I0S NAP 0.003645 0.4574 None
3 1L6O SER LEU LYS LEU MET THR THR VAL 0.008043 0.42414 None
4 2AMT 1AA 0.0251 0.41396 None
5 1FLM FMN 0.01653 0.41163 None
6 3KV8 FAH 0.04793 0.41128 None
7 4QVB F42 0.01092 0.42256 2.04082
8 1JIF CU BLM 0.03106 0.41439 2.45902
9 5LYH 7B8 0.02174 0.41964 2.72109
10 3UEC ALA ARG TPO LYS 0.006789 0.41129 2.73973
11 5X8G S0N 0.0436 0.42112 4.08163
12 5TA6 79D 0.03098 0.40977 4.08163
13 5IH9 6BF 0.00691 0.46001 5.44218
14 3A5Y KAA 0.01447 0.42113 5.44218
15 3A5Z KAA 0.01878 0.41433 5.44218
16 3VEH 0GA 0.02969 0.41861 6.12245
17 1USF FMN 0.02603 0.41287 6.12245
18 1USF NAP 0.03 0.41287 6.12245
19 4B2Z P5S 0.04205 0.40962 6.12245
20 2E5A LAQ 0.04135 0.40356 6.12245
21 3AHO 3A2 0.04166 0.40171 6.12245
22 3ZOD HQE 0.009821 0.43597 6.80272
23 3N0S ACO 0.01739 0.43274 6.80272
24 4P8K 38C 0.03957 0.42378 6.80272
25 3AFH GSU 0.01152 0.41537 6.80272
26 1AMU AMP 0.02833 0.40062 6.80272
27 4CS4 AXZ 0.02421 0.42528 10.8844
28 3BJK CIT 0.0358 0.41086 11.5646
29 4TXJ THM 0.01186 0.4286 12.2449
30 1PVC ILE SER GLU VAL 0.0007408 0.41559 25
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