Receptor
PDB id Resolution Class Description Source Keywords
2B56 1.97 Å NON-ENZYME: TRANSCRIPT_TRANSLATE STRUCTURAL BASIS FOR UTP SPECIFICITY OF RNA EDITING TUTASES TRYPANOSOMA BRUCEI TRYPANOSOMA BRUCEI TBRET2 TUTASE RNA EDITING TRANSFERASE TRYPANOSOMA BRUCEITRANSFERASE-RNA BINDING PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR UTP SPECIFICITY OF RNA EDITING FROM TRYPANOSOMA BRUCEI. EMBO J. V. 24 4007 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:488;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
U5P A:601;
A:602;
Valid;
Valid;
none;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
UTP A:501;
Valid;
none;
submit data
484.141 C9 H15 N2 O15 P3 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2B56 1.97 Å NON-ENZYME: TRANSCRIPT_TRANSLATE STRUCTURAL BASIS FOR UTP SPECIFICITY OF RNA EDITING TUTASES TRYPANOSOMA BRUCEI TRYPANOSOMA BRUCEI TBRET2 TUTASE RNA EDITING TRANSFERASE TRYPANOSOMA BRUCEITRANSFERASE-RNA BINDING PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR UTP SPECIFICITY OF RNA EDITING FROM TRYPANOSOMA BRUCEI. EMBO J. V. 24 4007 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 2B56 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 2B51 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 2B56 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 2B51 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 2B56 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 2B51 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
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
Ligand no: 2; Ligand: UTP; Similar ligands found: 114
No: Ligand ECFP6 Tc MDL keys Tc
1 UTP 1 1
2 UDP 0.892308 1
3 UNP 0.767123 0.970149
4 U5P 0.746269 0.984615
5 GDU 0.7125 0.941176
6 UPG 0.7125 0.941176
7 UFM 0.7125 0.941176
8 GUD 0.7125 0.941176
9 UPU 0.701299 0.940298
10 UPP 0.7 0.941176
11 UDH 0.7 0.864865
12 2KH 0.693333 0.970149
13 URM 0.691358 0.927536
14 660 0.691358 0.927536
15 44P 0.690141 0.955882
16 UFG 0.686747 0.888889
17 U2F 0.686747 0.888889
18 UPF 0.686747 0.888889
19 UAD 0.666667 0.941176
20 UDX 0.666667 0.941176
21 UDP UDP 0.662162 0.939394
22 3UC 0.655172 0.888889
23 UGA 0.651163 0.955224
24 USQ 0.651163 0.820513
25 UGB 0.651163 0.955224
26 G3N 0.643678 0.914286
27 CTP 0.620253 0.942029
28 UD1 0.619565 0.927536
29 UD2 0.619565 0.927536
30 UDM 0.615385 0.914286
31 UP5 0.602041 0.853333
32 DUT 0.6 0.913043
33 U 0.597015 0.863636
34 URI 0.597015 0.863636
35 UD7 0.589474 0.927536
36 HP7 0.589474 0.941176
37 Y6W 0.586207 0.888889
38 MJZ 0.583333 0.914286
39 UD4 0.57732 0.914286
40 HWU 0.57732 0.901408
41 12V 0.57732 0.901408
42 UDP GAL 0.573034 0.913043
43 IUG 0.565657 0.810127
44 EPZ 0.558824 0.914286
45 UDZ 0.554455 0.853333
46 EPU 0.553398 0.901408
47 EEB 0.553398 0.901408
48 CJB 0.549296 0.820895
49 CDP 0.54321 0.942029
50 4TC 0.528846 0.831169
51 U U 0.527473 0.955224
52 UA3 0.526316 0.939394
53 U3P 0.526316 0.939394
54 CSQ 0.515464 0.851351
55 CSV 0.515464 0.851351
56 UMA 0.513514 0.914286
57 U4S 0.512821 0.753425
58 DUD 0.512195 0.913043
59 CH 0.506329 0.913043
60 5GW 0.505618 0.942029
61 U2S 0.5 0.767123
62 U3S 0.5 0.753425
63 H6Y 0.48913 0.851351
64 U2P 0.487179 0.954545
65 U22 0.487179 0.790123
66 U21 0.487179 0.810127
67 U20 0.487179 0.810127
68 4GW 0.484211 0.915493
69 8GT 0.483516 0.855263
70 U1S 0.483146 0.75
71 2QR 0.478992 0.822785
72 PUP 0.473684 0.913043
73 C5G 0.46875 0.888889
74 DKX 0.467532 0.746479
75 5FU 0.45679 0.914286
76 A U 0.454545 0.805195
77 4RA 0.452381 0.855263
78 C2G 0.451613 0.901408
79 7XL 0.450549 0.888889
80 UAG 0.448819 0.864865
81 MGT 0.447917 0.780488
82 UD0 0.445312 0.844156
83 UMF 0.444444 0.857143
84 2TU 0.434211 0.774648
85 C5P 0.433735 0.927536
86 UMP 0.433735 0.898551
87 CAR 0.433735 0.927536
88 DU 0.433735 0.898551
89 C 0.433735 0.927536
90 2GW 0.432692 0.901408
91 U U U U 0.431579 0.940298
92 G8D 0.430108 0.855263
93 TTP 0.428571 0.875
94 CDM 0.428571 0.842105
95 5BU 0.428571 0.914286
96 UTP U U U 0.427083 0.895522
97 8OD 0.425532 0.851351
98 UC5 0.425287 0.9
99 N3E 0.425287 0.733333
100 91P 0.424779 0.802469
101 UUA 0.421053 0.772727
102 CXY 0.42 0.888889
103 CDC 0.418367 0.777778
104 1GW 0.418182 0.864865
105 DUP 0.417582 0.887324
106 CNU 0.413793 0.927536
107 DCP 0.413043 0.849315
108 UML 0.410072 0.810127
109 UPA 0.40708 0.842105
110 16B 0.406977 0.888889
111 D3T 0.406593 0.875
112 BMP 0.404762 0.970149
113 S5P 0.404762 0.915493
114 U2G 0.4 0.822785
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2B56; Ligand: UTP; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 2b56.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4U03 GTP 0.001565 0.40833 1.87354
2 3JYY PPV 0.003277 0.45538 2.43902
3 3JZ0 APC 0.005337 0.43088 2.43902
4 4XJ6 GH3 0.0001641 0.49283 3.1941
5 4CP9 GAL CN8 0.02222 0.41251 8.26446
6 1KNY APC 0.00356 0.43506 9.48617
7 3HIY UTP 0.00000002892 0.53317 11.4583
8 3HJ1 UTP 0.0000002799 0.5117 12.4031
9 5A2Z GTP 0.000006722 0.58758 14.1026
10 5W0N 2KH 0.0000001168 0.63856 18.6104
11 4NKT 2KH 0.0000000692 0.52196 25.5132
12 2Q0D ATP 0.0000000009786 0.67428 26.6289
13 5I49 2KH 0.0000001973 0.49068 43.1624
Pocket No.: 2; Query (leader) PDB : 2B56; Ligand: U5P; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 2b56.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4U03 GTP 0.001565 0.40833 1.87354
2 3B0X DGT 0.01045 0.42077 2.13675
3 3JYY PPV 0.003277 0.45538 2.43902
4 3JZ0 APC 0.005337 0.43088 2.43902
5 4XJ6 GH3 0.0001641 0.49283 3.1941
6 4CP9 GAL CN8 0.02222 0.41251 8.26446
7 1KNY APC 0.00356 0.43506 9.48617
8 3HIY UTP 0.00000002892 0.53317 11.4583
9 3HJ1 UTP 0.0000002799 0.5117 12.4031
10 5A2Z GTP 0.000006722 0.58758 14.1026
11 5W0N 2KH 0.0000001168 0.63856 18.6104
12 4NKT 2KH 0.0000000692 0.52196 25.5132
13 2Q0D ATP 0.0000000009786 0.61623 26.6289
14 5I49 2KH 0.0000001973 0.49068 43.1624
Pocket No.: 3; Query (leader) PDB : 2B56; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2b56.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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