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 308 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 266 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 220 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 (2D)
Ligand no: 1; Ligand: U5P; Similar ligands found: 125
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 U 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 U5F 0.735294 0.984615
8 UDP UDP 0.727273 0.953846
9 UPU 0.694444 0.954545
10 UNP 0.690141 0.955224
11 660 0.662338 0.913043
12 URM 0.662338 0.913043
13 URI 0.661017 0.848485
14 GDU 0.641026 0.926471
15 UFM 0.641026 0.926471
16 UPG 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 AWU 0.6125 0.926471
24 CJB 0.603175 0.80597
25 UDX 0.597561 0.926471
26 UDP GAL 0.597561 0.898551
27 UAD 0.597561 0.926471
28 3UC 0.588235 0.875
29 USQ 0.583333 0.807692
30 UGB 0.583333 0.940298
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 UGF 0.576471 0.887324
35 U3P 0.573529 0.953846
36 UA3 0.573529 0.953846
37 C 0.571429 0.941176
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 UD2 0.555556 0.913043
44 UD1 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U2S 0.541667 0.777778
48 U3S 0.541667 0.763889
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 FZK 0.530864 0.765432
53 U2P 0.528571 0.939394
54 UMP 0.527778 0.911765
55 DU 0.527778 0.911765
56 HP7 0.526882 0.926471
57 UD7 0.526882 0.913043
58 MJZ 0.521277 0.9
59 UP6 0.521127 0.884058
60 F5P 0.515789 0.9
61 12V 0.515789 0.887324
62 UD4 0.515789 0.9
63 F5G 0.515789 0.913043
64 HWU 0.515789 0.887324
65 BMP 0.513889 0.955224
66 UP5 0.510204 0.84
67 DKX 0.507246 0.732394
68 U6M 0.506849 0.969697
69 NUP 0.506849 0.927536
70 LSU 0.505882 0.746988
71 IUG 0.505155 0.797468
72 EPZ 0.5 0.9
73 JW5 0.5 0.955224
74 4TC 0.5 0.818182
75 U1S 0.5 0.76
76 EPU 0.49505 0.887324
77 EEB 0.49505 0.887324
78 UDZ 0.494949 0.84
79 H2U 0.486111 0.911765
80 YSU 0.483516 0.756098
81 6CN 0.480519 0.941176
82 OMP 0.480519 0.969697
83 6AU 0.480519 0.969697
84 TKW 0.48 0.927536
85 UMF 0.479452 0.869565
86 UUA 0.477612 0.757576
87 BMQ 0.472222 0.939394
88 PUP 0.47191 0.926471
89 5HM 0.467532 0.888889
90 O7E 0.463415 0.941176
91 ICR 0.460526 0.830986
92 UMA 0.458716 0.9
93 O7M 0.45679 0.941176
94 UC5 0.455696 0.885714
95 UTP U U U 0.454545 0.909091
96 CDP 0.45 0.927536
97 2TU 0.449275 0.760563
98 FNU 0.441558 0.876712
99 2TM 0.440476 0.888889
100 2QR 0.439655 0.810127
101 DUD 0.4375 0.898551
102 N3E 0.4375 0.743243
103 2OM 0.435897 0.925373
104 U21 0.434783 0.797468
105 U22 0.434783 0.777778
106 U20 0.434783 0.797468
107 HF4 0.433735 0.927536
108 CTP 0.433735 0.927536
109 DUT 0.433735 0.898551
110 8OP 0.428571 0.849315
111 BUP 0.428571 0.914286
112 8GM 0.421687 0.853333
113 5GW 0.420455 0.927536
114 CDP MG 0.414634 0.898551
115 4RA 0.414634 0.842105
116 0RC 0.413793 0.851351
117 DUP 0.411765 0.873239
118 DUN 0.409639 0.873239
119 UD0 0.408 0.831169
120 UM3 0.407895 0.897059
121 UVC 0.407895 0.842857
122 C5G 0.404255 0.875
123 6MZ C U 0.403226 0.775
124 UPA 0.401869 0.828947
125 UAG 0.4 0.851351
Ligand no: 2; Ligand: UTP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 UTP 1 1
2 U5F 0.984375 1
3 UDP 0.892308 1
4 UNP 0.767123 0.970149
5 U5P 0.746269 0.984615
6 U 0.746269 0.984615
7 UFM 0.7125 0.941176
8 UPG 0.7125 0.941176
9 GDU 0.7125 0.941176
10 UPU 0.701299 0.940298
11 UDH 0.7 0.864865
12 UPP 0.7 0.941176
13 2KH 0.693333 0.970149
14 URM 0.691358 0.927536
15 660 0.691358 0.927536
16 44P 0.690141 0.955882
17 UFG 0.686747 0.888889
18 U2F 0.686747 0.888889
19 UPF 0.686747 0.888889
20 AWU 0.682927 0.941176
21 UAD 0.666667 0.941176
22 UDX 0.666667 0.941176
23 UDP UDP 0.662162 0.939394
24 3UC 0.655172 0.888889
25 UGA 0.651163 0.955224
26 UGB 0.651163 0.955224
27 USQ 0.651163 0.820513
28 UGF 0.643678 0.901408
29 G3N 0.643678 0.914286
30 HF4 0.620253 0.942029
31 CTP 0.620253 0.942029
32 UD2 0.619565 0.927536
33 UD1 0.619565 0.927536
34 UDM 0.615385 0.914286
35 BUP 0.6125 0.928571
36 UP5 0.602041 0.853333
37 DUT 0.6 0.913043
38 URI 0.597015 0.863636
39 HP7 0.589474 0.941176
40 UD7 0.589474 0.927536
41 Y6W 0.586207 0.888889
42 MJZ 0.583333 0.914286
43 UD4 0.57732 0.914286
44 F5G 0.57732 0.927536
45 12V 0.57732 0.901408
46 HWU 0.57732 0.901408
47 F5P 0.57732 0.914286
48 UDP GAL 0.573034 0.913043
49 IUG 0.565657 0.810127
50 EPZ 0.558824 0.914286
51 UDZ 0.554455 0.853333
52 EPU 0.553398 0.901408
53 EEB 0.553398 0.901408
54 CJB 0.549296 0.820895
55 CDP 0.54321 0.942029
56 4TC 0.528846 0.831169
57 U3P 0.526316 0.939394
58 UA3 0.526316 0.939394
59 CSV 0.515464 0.851351
60 CSQ 0.515464 0.851351
61 UMA 0.513514 0.914286
62 U4S 0.512821 0.753425
63 DUD 0.512195 0.913043
64 5GW 0.505618 0.942029
65 U2S 0.5 0.767123
66 U3S 0.5 0.753425
67 FZK 0.494382 0.777778
68 H6Y 0.48913 0.851351
69 U21 0.487179 0.810127
70 U2P 0.487179 0.954545
71 U20 0.487179 0.810127
72 U22 0.487179 0.790123
73 4GW 0.484211 0.915493
74 8GT 0.483516 0.855263
75 U1S 0.483146 0.75
76 2QR 0.478992 0.822785
77 PUP 0.473684 0.913043
78 C5G 0.46875 0.888889
79 DKX 0.467532 0.746479
80 0RC 0.466667 0.864865
81 LSU 0.457447 0.738095
82 5FU 0.45679 0.914286
83 4RA 0.452381 0.855263
84 C2G 0.451613 0.901408
85 7XL 0.450549 0.888889
86 UAG 0.448819 0.864865
87 MGT 0.447917 0.780488
88 UD0 0.445312 0.844156
89 2TM 0.444444 0.902778
90 UMF 0.444444 0.857143
91 YSU 0.44 0.746988
92 2TU 0.434211 0.774648
93 CAR 0.433735 0.927536
94 C5P 0.433735 0.927536
95 C 0.433735 0.927536
96 UMP 0.433735 0.898551
97 DU 0.433735 0.898551
98 2GW 0.432692 0.901408
99 G8D 0.430108 0.855263
100 CDM 0.428571 0.842105
101 TTP 0.428571 0.875
102 5BU 0.428571 0.914286
103 UTP U U U 0.427083 0.895522
104 8OD 0.425532 0.851351
105 N3E 0.425287 0.733333
106 UC5 0.425287 0.9
107 91P 0.424779 0.802469
108 UUA 0.421053 0.772727
109 CXY 0.42 0.888889
110 PRT 0.419048 0.813333
111 CDC 0.418367 0.777778
112 1GW 0.418182 0.864865
113 DUP 0.417582 0.887324
114 CNU 0.413793 0.927536
115 DCP 0.413043 0.849315
116 UML 0.410072 0.810127
117 UPA 0.40708 0.842105
118 16B 0.406977 0.888889
119 D3T 0.406593 0.875
120 S5P 0.404762 0.915493
121 BMP 0.404762 0.970149
122 GTF 0.404255 0.849315
123 U2G 0.4 0.822785
Similar Ligands (3D)
Ligand no: 1; Ligand: U5P; Similar ligands found: 159
No: Ligand Similarity coefficient
1 CH 0.9980
2 PSU 0.9973
3 FN5 0.9948
4 TMP 0.9732
5 DUS 0.9718
6 DC 0.9664
7 DCM 0.9664
8 DDN 0.9644
9 DOC 0.9638
10 AMP 0.9607
11 PFU 0.9599
12 FDM 0.9594
13 UMC 0.9592
14 5IU 0.9586
15 NYM 0.9569
16 UFP 0.9556
17 QBT 0.9539
18 NIA 0.9524
19 C2R 0.9524
20 5CM 0.9522
21 BRU 0.9504
22 AMZ 0.9489
23 IRP 0.9478
24 IMP 0.9477
25 9L3 0.9467
26 AIR 0.9428
27 D4M 0.9413
28 2DT 0.9412
29 8BR 0.9372
30 LMS 0.9367
31 MZP 0.9362
32 RVP 0.9343
33 DA 0.9307
34 D5M 0.9307
35 FMP 0.9292
36 AS 0.9273
37 5GP 0.9224
38 5HU 0.9218
39 G 0.9216
40 NMN 0.9211
41 6MA 0.9211
42 NCN 0.9190
43 EO7 0.9189
44 IRN 0.9185
45 6RE 0.9182
46 J7C 0.9180
47 GAR 0.9171
48 XMP 0.9160
49 T3S 0.9160
50 DGP 0.9142
51 DG 0.9142
52 NEC 0.9123
53 M2T 0.9120
54 71V 0.9112
55 A3N 0.9101
56 IMU 0.9083
57 N5O 0.9067
58 Z8B 0.9047
59 6HW 0.9038
60 AOC 0.9029
61 ATM 0.9024
62 FAI 0.9014
63 EP4 0.9011
64 CTN 0.9002
65 JLN 0.8996
66 TDH 0.8991
67 6SY 0.8987
68 4UB 0.8973
69 7D5 0.8963
70 CMP 0.8944
71 BHF 0.8944
72 MTA 0.8934
73 PZB 0.8931
74 0SX 0.8928
75 TXS 0.8916
76 4ZK 0.8910
77 43J 0.8887
78 2T4 0.8886
79 XEZ 0.8883
80 9XZ 0.8879
81 362 0.8876
82 5QT 0.8869
83 FBP 0.8856
84 N8M 0.8853
85 O8M 0.8852
86 2GE 0.8842
87 NWQ 0.8838
88 CC7 0.8836
89 5UD 0.8830
90 VIB 0.8823
91 5AE 0.8814
92 I5A 0.8808
93 49K 0.8807
94 1TM 0.8807
95 IWH 0.8801
96 GEO 0.8799
97 103 0.8799
98 8OG 0.8796
99 43G 0.8783
100 SP1 0.8779
101 DRM 0.8774
102 URD 0.8759
103 14I 0.8755
104 RP1 0.8747
105 AFP 0.8738
106 6HV 0.8726
107 KWQ 0.8724
108 VKE 0.8724
109 HDU 0.8720
110 DUR 0.8710
111 K8W 0.8707
112 AHG 0.8702
113 90J 0.8699
114 1CE 0.8694
115 F01 0.8687
116 TYU 0.8678
117 FT1 0.8676
118 74Z 0.8675
119 6HZ 0.8674
120 HKK 0.8672
121 ML2 0.8669
122 F0G 0.8645
123 101 0.8644
124 PCG 0.8636
125 GG5 0.8631
126 3DV 0.8626
127 TYD 0.8621
128 T1D 0.8620
129 BL6 0.8617
130 HM5 0.8614
131 CA0 0.8614
132 CQU 0.8613
133 ADN 0.8606
134 YM6 0.8605
135 DCZ 0.8604
136 RVA 0.8603
137 T7O 0.8598
138 8G6 0.8596
139 HNA 0.8592
140 9W8 0.8591
141 YTZ 0.8588
142 4BH 0.8585
143 7MF 0.8580
144 K6B 0.8580
145 SW4 0.8576
146 ISJ 0.8576
147 ML1 0.8574
148 TBD 0.8568
149 ROL 0.8566
150 QTK 0.8555
151 K6N 0.8551
152 8RK 0.8549
153 YEX 0.8541
154 43F 0.8538
155 08D 0.8536
156 QTV 0.8529
157 JHY 0.8511
158 AD3 0.8509
159 90G 0.8508
Ligand no: 2; Ligand: UTP; Similar ligands found: 39
No: Ligand Similarity coefficient
1 DCP MG 0.9518
2 DCT 0.9455
3 ANP 0.9434
4 ATP 0.9337
5 BEF ADP 0.9318
6 DTP 0.9313
7 ACP 0.9261
8 AGS 0.9231
9 GTP 0.9210
10 GNP 0.9203
11 DUT MG 0.9178
12 3AT 0.9158
13 GSP 0.9143
14 F6G 0.9104
15 APC 0.9039
16 GDP BEF 0.9026
17 GCP 0.9022
18 BEF GDP 0.9003
19 ADP ALF 0.8993
20 DBG 0.8957
21 GDP ALF 0.8949
22 GH3 0.8948
23 9GM 0.8937
24 ALF GDP 0.8931
25 GDP AF3 0.8890
26 HQ5 0.8790
27 DGT 0.8773
28 HEJ 0.8768
29 TAT 0.8726
30 CDP MG 0.8720
31 L3U 0.8714
32 TYD 0.8698
33 ATF 0.8669
34 0KX 0.8668
35 ADP BEF 0.8633
36 ADP 0.8603
37 YYY 0.8596
38 JSQ 0.8556
39 ADP AF3 0.8554
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2B56; Ligand: UTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2b56.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2B56; Ligand: U5P; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2b56.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2B56; Ligand: U5P; Similar sites found with APoc: 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 Sequence Similarity
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