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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 1443 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 1205 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 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: U5P; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 U 1 1
2 U5P 1 1
3 44P 0.790323 0.941176
4 UDP 0.78125 0.984615
5 UTP 0.746269 0.984615
6 2KH 0.735294 0.955224
7 UDP UDP 0.727273 0.953846
8 UPU 0.694444 0.954545
9 UNP 0.690141 0.955224
10 660 0.662338 0.913043
11 URM 0.662338 0.913043
12 URI 0.661017 0.848485
13 GUD 0.641026 0.926471
14 UFM 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GDU 0.641026 0.926471
17 UPF 0.6375 0.875
18 U2F 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 3UC 0.588235 0.875
27 U U 0.585366 0.969697
28 UGB 0.583333 0.940298
29 USQ 0.583333 0.807692
30 UGA 0.583333 0.940298
31 5FU 0.57971 0.927536
32 G3N 0.576471 0.9
33 UA3 0.573529 0.953846
34 U3P 0.573529 0.953846
35 CAR 0.571429 0.941176
36 C 0.571429 0.941176
37 C5P 0.571429 0.941176
38 UDM 0.568182 0.9
39 5BU 0.56338 0.927536
40 U4S 0.557143 0.763889
41 UD1 0.555556 0.913043
42 UD2 0.555556 0.913043
43 CSQ 0.550562 0.863014
44 CSV 0.550562 0.863014
45 U2S 0.541667 0.777778
46 U3S 0.541667 0.763889
47 CNU 0.540541 0.941176
48 S5P 0.535211 0.901408
49 16B 0.534247 0.901408
50 U2P 0.528571 0.939394
51 DU 0.527778 0.911765
52 UMP 0.527778 0.911765
53 HP7 0.526882 0.926471
54 UD7 0.526882 0.913043
55 MJZ 0.521277 0.9
56 UP6 0.521127 0.884058
57 12V 0.515789 0.887324
58 F5G 0.515789 0.913043
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 F5P 0.515789 0.9
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 NUP 0.506849 0.927536
66 U6M 0.506849 0.969697
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 4TC 0.5 0.818182
71 JW5 0.5 0.955224
72 EEB 0.49505 0.887324
73 A U 0.49505 0.815789
74 EPU 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 OMP 0.480519 0.969697
78 6AU 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 G U 0.471154 0.797468
87 5HM 0.467532 0.888889
88 O7E 0.463415 0.941176
89 ICR 0.460526 0.830986
90 UMA 0.458716 0.9
91 O7M 0.45679 0.941176
92 UC5 0.455696 0.885714
93 UTP U U U 0.454545 0.909091
94 CDP 0.45 0.927536
95 2TU 0.449275 0.760563
96 FNU 0.441558 0.876712
97 2QR 0.439655 0.810127
98 DUD 0.4375 0.898551
99 N3E 0.4375 0.743243
100 2OM 0.435897 0.925373
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 U22 0.434783 0.777778
104 DUT 0.433735 0.898551
105 HF4 0.433735 0.927536
106 CTP 0.433735 0.927536
107 8OP 0.428571 0.849315
108 8GM 0.421687 0.853333
109 5GW 0.420455 0.927536
110 U A A U 0.418803 0.853333
111 4RA 0.414634 0.842105
112 DUP 0.411765 0.873239
113 DUN 0.409639 0.873239
114 UD0 0.408 0.831169
115 UVC 0.407895 0.842857
116 UM3 0.407895 0.897059
117 C5G 0.404255 0.875
118 UPA 0.401869 0.828947
119 A U C C 0.401639 0.794872
120 UAG 0.4 0.851351
121 A G U 0.4 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4G0P; Ligand: U5P; Similar sites found with APoc: 62
This union binding pocket(no: 1) in the query (biounit: 4g0p.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1I0S NAP None
2 1I0S FMN None
3 2Q16 ITT None
4 1L6O SER LEU LYS LEU MET THR THR VAL None
5 1FLM FMN None
6 3KV8 FAH None
7 2AMT 1AA None
8 1Q3P GLU ALA GLN THR ARG LEU None
9 5KHD C2E None
10 4QVB F42 2.04082
11 3IQE F42 2.04082
12 5UJ3 CE4 2.04082
13 3IQE H4M 2.04082
14 1JIF CU BLM 2.45902
15 4LCN GNG 2.72109
16 2UZH CDP 2.72109
17 3UEC ALA ARG TPO LYS 2.73973
18 2FXU BID 4.08163
19 5X8G S0N 4.08163
20 3NEM AMO 4.08163
21 5TA6 79D 4.08163
22 4JLS 3ZE 4.7619
23 5N81 8Q2 4.7619
24 4UBT COA 4.7619
25 2VJ8 HA2 4.7619
26 3A5Y KAA 5.44218
27 3A5Z KAA 5.44218
28 4HMT NNV 5.44218
29 4HMT FMN 5.44218
30 3A4T SFG 5.44218
31 3VEH 0GA 6.12245
32 1USF NAP 6.12245
33 1USF FMN 6.12245
34 6ECT SAM 6.12245
35 4B2Z P5S 6.12245
36 2E5A LAQ 6.12245
37 3AHO 3A2 6.12245
38 3HLF SIM 6.12245
39 3ZOD FMN 6.80272
40 3ZOD HQE 6.80272
41 3AFH GSU 6.80272
42 1T9M FMN 6.80272
43 4B5P ACO 6.80272
44 1AMU AMP 6.80272
45 1BHX ASP PHE GLU GLU ILE 8.84354
46 3N3T C2E 8.84354
47 3WB0 FEG 9.52381
48 5UBG PRT 11.5646
49 3BJK CIT 11.5646
50 1D6H COA 12.2449
51 4TXJ THM 12.2449
52 5MLJ 9ST 13.3929
53 2QJY SMA 13.6054
54 1OPK P16 13.6054
55 1XL8 OCB 13.6054
56 4XF6 INS 16.3265
57 4XF6 LIP 16.3265
58 4XF6 ADP 16.3265
59 4CPZ ZMR 16.3265
60 3K37 BCZ 16.3265
61 1PVC ILE SER GLU VAL 25
62 3HV8 C2E 25.1701
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