-->
Receptor
PDB id Resolution Class Description Source Keywords
5W0N 2.5 Å EC: 2.7.7.52 STRUCTURE OF HUMAN TUT7 CATALYTIC MODULE (CM) IN COMPLEX WIT AND U2 RNA HOMO SAPIENS TERMINAL URIDYLTRANSFERASE TUTASE TRANSFERASE
Ref.: MULTI-DOMAIN UTILIZATION BY TUT4 AND TUT7 IN CONTRO LET-7 BIOGENESIS. NAT. STRUCT. MOL. BIOL. V. 24 658 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:1404;
A:1404;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
MG B:1401;
C:1401;
A:1401;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:1406;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
2KH A:1402;
C:1402;
B:1402;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
IOD C:1404;
A:1405;
B:1405;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
126.904 I [I-]
UPU A:1403;
C:1403;
B:1403;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
550.367 C18 H23 N4 O14 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W0N 2.5 Å EC: 2.7.7.52 STRUCTURE OF HUMAN TUT7 CATALYTIC MODULE (CM) IN COMPLEX WIT AND U2 RNA HOMO SAPIENS TERMINAL URIDYLTRANSFERASE TUTASE TRANSFERASE
Ref.: MULTI-DOMAIN UTILIZATION BY TUT4 AND TUT7 IN CONTRO LET-7 BIOGENESIS. NAT. STRUCT. MOL. BIOL. V. 24 658 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5W0N - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5W0N - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5W0N - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2KH; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 2KH 1 1
2 U 0.735294 0.955224
3 U5P 0.735294 0.955224
4 UDP 0.722222 0.970149
5 UNP 0.710526 1
6 UTP 0.693333 0.970149
7 44P 0.680556 0.928571
8 UDP UDP 0.653333 0.911765
9 UPU 0.609756 0.913043
10 URM 0.604651 0.901408
11 660 0.604651 0.901408
12 GUD 0.586207 0.914286
13 GDU 0.586207 0.914286
14 UPG 0.586207 0.914286
15 UFM 0.586207 0.914286
16 DUP 0.585366 0.915493
17 UPP 0.574713 0.914286
18 UDH 0.574713 0.842105
19 UFG 0.566667 0.864865
20 UPF 0.566667 0.864865
21 U2F 0.566667 0.864865
22 URI 0.565217 0.838235
23 Y6W 0.561798 0.864865
24 UAD 0.549451 0.914286
25 UDX 0.549451 0.914286
26 3UC 0.542553 0.864865
27 UDM 0.541667 0.888889
28 UGA 0.537634 0.927536
29 USQ 0.537634 0.8
30 UGB 0.537634 0.927536
31 G3N 0.531915 0.888889
32 UD2 0.530612 0.901408
33 UD1 0.530612 0.901408
34 U U 0.521739 0.927536
35 CJB 0.520548 0.797101
36 UD7 0.504951 0.901408
37 HP7 0.504951 0.914286
38 MJZ 0.5 0.888889
39 U3P 0.5 0.911765
40 UA3 0.5 0.911765
41 HWU 0.495146 0.876712
42 12V 0.495146 0.876712
43 F5G 0.495146 0.901408
44 UD4 0.495146 0.888889
45 F5P 0.495146 0.888889
46 CSV 0.494949 0.828947
47 CSQ 0.494949 0.828947
48 U4S 0.4875 0.733333
49 EPZ 0.481481 0.888889
50 EPU 0.477064 0.876712
51 EEB 0.477064 0.876712
52 UP5 0.476636 0.831169
53 UDZ 0.476636 0.88
54 U2S 0.47561 0.746667
55 U3S 0.47561 0.733333
56 IUG 0.471698 0.835443
57 U2P 0.4625 0.926471
58 U1S 0.461538 0.730769
59 DUN 0.45977 0.915493
60 4TC 0.454545 0.810127
61 UMA 0.444444 0.888889
62 DKX 0.443038 0.726027
63 5BU 0.440476 0.888889
64 PUP 0.438776 0.887324
65 A U 0.4375 0.78481
66 5FU 0.433735 0.888889
67 CDP 0.431818 0.915493
68 G U 0.429825 0.768293
69 C 0.428571 0.901408
70 C5P 0.428571 0.901408
71 CAR 0.428571 0.901408
72 U U U U 0.427083 0.913043
73 U21 0.422764 0.790123
74 U22 0.422764 0.771084
75 U20 0.422764 0.790123
76 UTP U U U 0.42268 0.869565
77 UMF 0.421687 0.833333
78 DUD 0.420455 0.887324
79 16B 0.418605 0.890411
80 CTP 0.417582 0.915493
81 DUT 0.417582 0.887324
82 HF4 0.417582 0.915493
83 2QR 0.416 0.802469
84 UUA 0.415584 0.75
85 UMP 0.411765 0.873239
86 DU 0.411765 0.873239
87 CNU 0.409091 0.901408
88 5GW 0.40625 0.915493
89 4RA 0.40458 0.833333
90 N3E 0.404494 0.714286
91 UC5 0.404494 0.875
92 S5P 0.4 0.890411
Ligand no: 2; Ligand: UPU; Similar ligands found: 106
No: Ligand ECFP6 Tc MDL keys Tc
1 UPU 1 1
2 UDP 0.72973 0.940298
3 UTP 0.701299 0.940298
4 U5P 0.694444 0.954545
5 U 0.694444 0.954545
6 UA3 0.680556 0.939394
7 U3P 0.680556 0.939394
8 660 0.670588 0.955882
9 URM 0.670588 0.955882
10 UPG 0.670588 0.970149
11 UFM 0.670588 0.970149
12 GUD 0.670588 0.970149
13 GDU 0.670588 0.970149
14 UNP 0.654321 0.913043
15 U2F 0.647727 0.915493
16 UPF 0.647727 0.915493
17 44P 0.644737 0.9
18 PUP 0.629214 0.913043
19 UFG 0.629214 0.915493
20 CSV 0.617021 0.902778
21 UDM 0.617021 0.942029
22 CSQ 0.617021 0.902778
23 UAD 0.611111 0.941176
24 UDX 0.611111 0.941176
25 2KH 0.609756 0.913043
26 UPP 0.602273 0.941176
27 UDH 0.602273 0.864865
28 3UC 0.602151 0.915493
29 UDP UDP 0.6 0.939394
30 URI 0.6 0.863636
31 U U 0.6 0.955224
32 Y6W 0.588889 0.915493
33 UD2 0.587629 0.955882
34 UD1 0.587629 0.955882
35 UGA 0.580645 0.955224
36 USQ 0.580645 0.820513
37 UGB 0.580645 0.955224
38 G3N 0.574468 0.914286
39 CJB 0.554054 0.848485
40 12V 0.533981 0.928571
41 HWU 0.533981 0.928571
42 EPZ 0.53271 0.942029
43 UD7 0.529412 0.927536
44 HP7 0.529412 0.941176
45 EEB 0.527778 0.928571
46 EPU 0.527778 0.928571
47 APU 0.527778 0.853333
48 MJZ 0.524272 0.914286
49 F5P 0.519231 0.914286
50 UD4 0.519231 0.914286
51 F5G 0.519231 0.927536
52 UDZ 0.514019 0.853333
53 U2P 0.5125 0.925373
54 IUG 0.509434 0.810127
55 UP5 0.5 0.853333
56 U U U U 0.5 0.940298
57 UMA 0.491379 0.942029
58 G U 0.491071 0.810127
59 4TC 0.490909 0.831169
60 A U 0.486486 0.853333
61 U2G 0.482143 0.822785
62 U4S 0.481928 0.753425
63 UTP U U U 0.479167 0.924242
64 UPA 0.477477 0.866667
65 DKX 0.475 0.771429
66 U2S 0.470588 0.791667
67 U3S 0.470588 0.777778
68 UMF 0.46988 0.857143
69 U21 0.467213 0.833333
70 U22 0.467213 0.8125
71 U20 0.467213 0.833333
72 UCG 0.455285 0.797468
73 U A A U 0.451613 0.842105
74 C5G 0.445545 0.915493
75 CDP 0.444444 0.887324
76 2TU 0.443038 0.774648
77 U1S 0.442105 0.773333
78 C C C C 0.44 0.914286
79 2QR 0.436508 0.822785
80 A U C C 0.434109 0.831169
81 GPC 0.433333 0.792683
82 UAG 0.431818 0.890411
83 5FU 0.430233 0.887324
84 HF4 0.430108 0.887324
85 CTP 0.430108 0.887324
86 5GW 0.418367 0.914286
87 U A 0.418033 0.842105
88 DUD 0.417582 0.859155
89 A G U U 0.416058 0.8
90 DUT 0.414894 0.859155
91 4RA 0.413534 0.831169
92 2GW 0.412844 0.928571
93 UUA 0.4125 0.746269
94 7XL 0.412371 0.888889
95 A G U 0.410448 0.8
96 C5P 0.409091 0.9
97 UMP 0.409091 0.871429
98 DU 0.409091 0.871429
99 C 0.409091 0.9
100 CAR 0.409091 0.9
101 UD0 0.407407 0.820513
102 5BU 0.404494 0.887324
103 G U34 0.403361 0.8
104 UC5 0.402174 0.847222
105 N3E 0.402174 0.780822
106 C2G 0.4 0.901408
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W0N; Ligand: UPU; Similar sites found with APoc: 185
This union binding pocket(no: 1) in the query (biounit: 5w0n.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1IDA 0PO None
2 2RFZ CTR 1.48883
3 4ER2 IVA VAL VAL STA ALA STA 1.51515
4 2WSA 646 1.73697
5 2WSA MYA 1.73697
6 6G0X RAM GLC GLA NAG NDG NAG 1.73697
7 5XWC 2IT 1.73697
8 5XWC 8GL 1.73697
9 5XWC NAP 1.73697
10 4WUP 3UF 1.92308
11 6A1G 9OL 1.94444
12 5GUD 2IT 1.98511
13 5GUD NDP 1.98511
14 4JYD SAH 2.01149
15 1ZZ7 S0H 2.0202
16 4U0W 16G 2.03252
17 3CTL S6P 2.1645
18 4F4P 0SB 2.1978
19 1YKD CMP 2.26131
20 5F2T PLM 2.27273
21 3WW2 SF6 2.34375
22 3WW2 LPK 2.34375
23 3FSM 2NC 2.46305
24 3KA2 2NC 2.46305
25 4U03 GTP 2.48139
26 4U03 TLL 2.48139
27 4ZL4 4PK 2.48139
28 2CJF RP4 2.54777
29 1ZAP A70 2.63158
30 5W4W 9WG 2.71903
31 2OVD DAO 2.74725
32 1IZE IVA VAL VAL STA ALA STA 2.78638
33 4QDC ASD 2.82051
34 4TWL ASC 2.84553
35 1FMB HYB 2.88462
36 5XDT ZI7 2.92208
37 5DOZ NDP 2.95858
38 1IS3 LAT 2.96296
39 2D3M COA 2.97767
40 4A4X JUP 2.97767
41 4LED XXR 2.98507
42 3MWS 017 3.0303
43 5DRB 5FJ 3.09278
44 5TZO 7V7 3.19149
45 5HA0 LTD 3.20513
46 5X7Q GLC GLC GLC GLC GLC 3.22581
47 3TMK T5A 3.24074
48 5CFT 51G 3.24324
49 4MP8 MLI 3.24484
50 4MP8 NAD 3.24484
51 5D48 L96 3.28947
52 1ODM ASV 3.32326
53 1I06 TZL 3.33333
54 5E2N V14 3.42205
55 4IX4 ADP 3.42857
56 1QY1 PRZ 3.44828
57 2VOT NHV 3.47395
58 3PG7 PTY 3.51562
59 1WKR IVA VAL VAL STA ALA STA 3.52941
60 4OIT BMA 3.53982
61 1XLI GLT 3.5533
62 1IA9 ANP 3.57143
63 5IH9 6BF 3.58209
64 6D61 4AA 3.58974
65 1Q23 FUA 3.65297
66 1OLM VTQ 3.72208
67 2PYW ADP 3.72208
68 4MNS 2AX 3.77358
69 5ANU 58T 3.79747
70 5NEA 8V8 3.84615
71 4BVA NDP 3.8806
72 5UWA 8ND 3.94089
73 5AIG VPR 4
74 5GP0 GPP 4.02685
75 5ML3 DL3 4.02685
76 3FPF MTA 4.02685
77 3FPF TNA 4.02685
78 3WDX BGC BGC GLC 4.02685
79 4D4U FUC NDG GAL FUC 4.12698
80 1SMR PIV HIS PRO PHE HIS LPL TYR TYR SER 4.1791
81 2PTZ PAH 4.21836
82 3STD MQ0 4.24242
83 3HDY FDA 4.28212
84 3HDY GDU 4.28212
85 3HDY FAD 4.28212
86 2PUL ACP 4.28212
87 5Z6T NAP 4.37318
88 3WUC GLC GAL 4.37956
89 3WV6 GAL BGC 4.39189
90 3E8N ATP 4.39883
91 3E8N VRA 4.39883
92 1GT4 UNA 4.40252
93 2D6M LBT 4.40252
94 2F59 INI 4.4586
95 1SLT NDG GAL 4.47761
96 2VQ5 HBA 4.47761
97 3STK PLM 4.54545
98 2FLI DX5 4.54545
99 1ZM1 BGC BGC BGC 4.56432
100 6CAY ERG 4.73373
101 5TIV A3P 4.74308
102 3JUQ AKD 4.86486
103 3JUQ AJD 4.86486
104 2XK9 XK9 4.96894
105 4Q0P 0MK 5
106 2AMT 1AA 5.03145
107 2AMT GPP 5.03145
108 6C8X BVR 5.05051
109 5T2Z 017 5.05051
110 3NWQ 2NC 5.05051
111 2P3B 3TL 5.05051
112 4NJS G08 5.05051
113 3SCH TB6 5.05051
114 4NPT 017 5.05051
115 2GQS ADP 5.06329
116 3GC8 B45 5.13514
117 5H9Q TD2 5.16129
118 4WW8 VD9 5.32319
119 4OMJ 2TX 5.39568
120 4LOO SB4 5.54017
121 1IND EOT 5.5814
122 3SAO NKN 5.625
123 2YG2 S1P 5.81395
124 4XV1 904 5.82192
125 1Y7P RIP 5.8296
126 2YGO PCF 5.85106
127 3ILR SGN 5.94595
128 3ILR IXD 5.94595
129 1NWW HPN 6.04027
130 1U0A BGC BGC BGC BGC 6.07477
131 4ITH RCM 6.12245
132 4ZSI GLP 6.43275
133 4ZSI 4R1 6.43275
134 4N02 FNR 6.44258
135 3W8X FTK 6.45161
136 3W8X FAD 6.45161
137 5NLD LBT 6.47482
138 5DG2 GAL GLC 6.66667
139 3N0Y APC 6.70391
140 4Q5M ROC 6.89655
141 2YMZ LAT 6.92308
142 4WVW SLT 6.94444
143 5VGS 9A4 7.00637
144 2YGN PCF 7.05128
145 5WRE 7TL 7.74194
146 2GQR ADP 8.01688
147 3ZW2 GLA NAG GAL FUC 8.04598
148 2P3C 3TL 8.08081
149 4M8X KGQ 8.08081
150 5I8T LAC 8.37989
151 2Q7D ANP 8.3815
152 2R0H CTO 8.53659
153 5XNC N4P 8.62534
154 2CM4 RCL 9.33333
155 2IXC TRH 9.40594
156 3NV3 GAL NAG MAN 9.42029
157 4M1U A2G MBG 10
158 1SIV PSI 10.101
159 5EZU MYR 10.1124
160 1Q79 3AT 10.9181
161 1A78 TDG 11.194
162 4IPH 1FJ 11.3821
163 1Z0N BCD 11.4583
164 6FIV 3TL 11.5044
165 4XIZ LPP 11.7647
166 1ULE GLA GAL NAG 12
167 3S43 478 12.1212
168 3L9R L9Q 12.2449
169 3L9R L9R 12.2449
170 1DZK PRZ 12.7389
171 1UNB PN1 13.8264
172 1UNB AKG 13.8264
173 4WO4 JLS 14
174 4PSB GA3 14.1935
175 5DQ8 FLF 14.5833
176 1QIN GIP 16.3934
177 1KJ1 MAN 16.5138
178 3GGU 017 18.1818
179 2O4N TPV 18.1818
180 3WUD GLC GAL 19.1176
181 2BOS GLA GAL GLC 19.1176
182 5K2M ADP 20.7547
183 2XN5 FUN 25.7143
184 1BHX ASP PHE GLU GLU ILE 30
185 1EB1 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 33.3333
Pocket No.: 2; Query (leader) PDB : 5W0N; Ligand: 2KH; Similar sites found with APoc: 50
This union binding pocket(no: 2) in the query (biounit: 5w0n.bio3) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5VE5 GSH 1.06101
2 3C3N FMN 1.60256
3 4UP4 GAL NAG 1.99501
4 3ICT FAD 2.21088
5 2XHK AKG 2.25225
6 4U03 GTP 2.48139
7 4U03 TLL 2.48139
8 5G3U ITW 2.48139
9 5G3U FDA 2.48139
10 5ZBC FAD 2.48139
11 4JBL MET 2.65487
12 3ZNN 4WL 2.88184
13 3ZNN FAD 2.88184
14 4DBH OXL 3.125
15 1YY5 FAD 3.47395
16 3NYC FAD 3.67454
17 3NYC IAR 3.67454
18 6FOG OXL 4.46429
19 3V1U NAD 4.4665
20 4TQK NAG 4.71464
21 4P4M D3T 4.7619
22 4XJ6 GH3 5.21092
23 2CDU FAD 5.45906
24 1KNY APC 5.5336
25 5LPA ATP 5.55556
26 5LPA 71R 5.55556
27 4OAG ADP 5.67164
28 3ER9 3AT 5.72391
29 4JLZ UTP 6.55738
30 2WET FAD 6.69975
31 4BC5 5FX 6.69975
32 2V5E SCR 6.93069
33 4X7Y SAH 6.93431
34 3JZ0 APC 6.96864
35 5WRE 7TL 7.74194
36 2JFV FLC 7.90378
37 3JYY PPV 8.01394
38 3B0X DGT 8.933
39 4CPB GAL CN8 10.7438
40 1Q79 3AT 10.9181
41 3LA3 2FT 11.5226
42 5LV1 78T 13.9286
43 3N39 FMN 17.2414
44 2B56 UTP 18.6104
45 2B56 U5P 18.6104
46 5I49 2KH 22.0844
47 3HIY UTP 36.7188
48 3HJ1 UTP 37.4677
49 5A2Z GTP 38.9578
50 4NKT 2KH 49.2669
Pocket No.: 3; Query (leader) PDB : 5W0N; Ligand: 2KH; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 5w0n.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 6BKK 308 None
2 3GD4 FAD 2.48139
3 1PIG GLC GLC 4.21836
4 3WV6 GAL GLC 4.39189
5 4MUQ LY0 5.09804
6 4MUS LY0 6.16114
7 1R89 CTP 6.86499
8 3N7S 3N7 7.82609
Pocket No.: 4; Query (leader) PDB : 5W0N; Ligand: UPU; Similar sites found with APoc: 24
This union binding pocket(no: 4) in the query (biounit: 5w0n.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1WMA NDP 1.44928
2 1WMA AB3 1.44928
3 4FFG 0U8 1.48883
4 3ZDS OMD 1.73697
5 5O98 NAP 1.89274
6 3T3Z 9PL 1.98511
7 6B9R 2HE 2.48139
8 3NW7 LGV 2.60586
9 3O26 NDP 2.89389
10 5W1E PHB 3.04183
11 1OFZ FUC 3.20513
12 6B9T 2HE 3.22581
13 2UVF AD0 3.47395
14 3PPQ CHT 3.85852
15 2E56 MYR 4.16667
16 3ZXE PGZ 4.51128
17 5L4S 6KX 4.71698
18 5L4S NAP 4.71698
19 4XJ6 GH3 5.21092
20 3KFF XBT 5.55556
21 3KFF ZBT 5.55556
22 4YHQ G10 7.07071
23 6GNO XDI 8.14815
24 5WP4 PC 18.8586
Pocket No.: 5; Query (leader) PDB : 5W0N; Ligand: 2KH; Similar sites found with APoc: 15
This union binding pocket(no: 5) in the query (biounit: 5w0n.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3ICR FAD 2.21088
2 3ICS FAD 2.21088
3 4NTD FAD 2.64706
4 3WGT QSC 2.88184
5 3WGT FAD 2.88184
6 6EBQ FMN 4.375
7 4EIP FAD 4.4665
8 2NPX NAD 4.96278
9 2Z3Y F2N 6.45161
10 2VVL FAD 6.45161
11 1RYI FAD 8.37696
12 1RYI GOA 8.37696
13 3KP6 SAL 8.60927
14 3KRB NAP 13.4731
15 2XKO AKG 23.5955
Pocket No.: 6; Query (leader) PDB : 5W0N; Ligand: UPU; Similar sites found with APoc: 13
This union binding pocket(no: 6) in the query (biounit: 5w0n.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 2OBD 2OB 1.73697
3 3K5I AIR 2.72953
4 3HPY MCT 3.55987
5 1J3R 6PG 3.68421
6 3G5N PB2 4.71464
7 5L13 6ZE 5.7072
8 1TKB N1T 6.20347
9 5VGS 9A7 7.00637
10 3WSJ MK1 8.62069
11 2R5N TPP 8.68486
12 2R5N RP5 8.68486
13 3T3C 017 13.1313
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