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 2 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 2 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 2 families.
1 5W0N - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2KH; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 2KH 1 1
2 U5P 0.735294 0.955224
3 UDP 0.722222 0.970149
4 UNP 0.710526 1
5 UTP 0.693333 0.970149
6 44P 0.680556 0.928571
7 UDP UDP 0.653333 0.911765
8 UPU 0.609756 0.913043
9 URM 0.604651 0.901408
10 660 0.604651 0.901408
11 GDU 0.586207 0.914286
12 UFM 0.586207 0.914286
13 UPG 0.586207 0.914286
14 GUD 0.586207 0.914286
15 DUP 0.585366 0.915493
16 UPP 0.574713 0.914286
17 UDH 0.574713 0.842105
18 UPF 0.566667 0.864865
19 UFG 0.566667 0.864865
20 U2F 0.566667 0.864865
21 U 0.565217 0.838235
22 URI 0.565217 0.838235
23 Y6W 0.561798 0.864865
24 UDP GAL 0.549451 0.887324
25 UDX 0.549451 0.914286
26 UAD 0.549451 0.914286
27 3UC 0.542553 0.864865
28 UDM 0.541667 0.888889
29 UGA 0.537634 0.927536
30 UGB 0.537634 0.927536
31 USQ 0.537634 0.8
32 G3N 0.531915 0.888889
33 UD2 0.530612 0.901408
34 UD1 0.530612 0.901408
35 U U 0.521739 0.927536
36 CJB 0.520548 0.797101
37 HP7 0.504951 0.914286
38 UD7 0.504951 0.901408
39 U3P 0.5 0.911765
40 CH 0.5 0.887324
41 UA3 0.5 0.911765
42 MJZ 0.5 0.888889
43 12V 0.495146 0.876712
44 HWU 0.495146 0.876712
45 UD4 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 EEB 0.477064 0.876712
51 EPU 0.477064 0.876712
52 UP5 0.476636 0.831169
53 UDZ 0.476636 0.88
54 U3S 0.47561 0.733333
55 U2S 0.47561 0.746667
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 CAR 0.428571 0.901408
69 C 0.428571 0.901408
70 C5P 0.428571 0.901408
71 U U U U 0.427083 0.913043
72 U20 0.422764 0.790123
73 U21 0.422764 0.790123
74 U22 0.422764 0.771084
75 UTP U U U 0.42268 0.869565
76 UMF 0.421687 0.833333
77 DUD 0.420455 0.887324
78 16B 0.418605 0.890411
79 CTP 0.417582 0.915493
80 DUT 0.417582 0.887324
81 2QR 0.416 0.802469
82 UUA 0.415584 0.75
83 DU 0.411765 0.873239
84 UMP 0.411765 0.873239
85 CNU 0.409091 0.901408
86 5GW 0.40625 0.915493
87 4RA 0.40458 0.833333
88 N3E 0.404494 0.714286
89 UC5 0.404494 0.875
90 S5P 0.4 0.890411
Ligand no: 2; Ligand: UPU; Similar ligands found: 102
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 UA3 0.680556 0.939394
6 U3P 0.680556 0.939394
7 UFM 0.670588 0.970149
8 URM 0.670588 0.955882
9 660 0.670588 0.955882
10 GUD 0.670588 0.970149
11 UPG 0.670588 0.970149
12 GDU 0.670588 0.970149
13 UNP 0.654321 0.913043
14 UPF 0.647727 0.915493
15 U2F 0.647727 0.915493
16 44P 0.644737 0.9
17 UFG 0.629214 0.915493
18 PUP 0.629214 0.913043
19 UDM 0.617021 0.942029
20 CSQ 0.617021 0.902778
21 CSV 0.617021 0.902778
22 UDX 0.611111 0.941176
23 UAD 0.611111 0.941176
24 2KH 0.609756 0.913043
25 UPP 0.602273 0.941176
26 UDH 0.602273 0.864865
27 3UC 0.602151 0.915493
28 U U 0.6 0.955224
29 U 0.6 0.863636
30 URI 0.6 0.863636
31 UDP UDP 0.6 0.939394
32 Y6W 0.588889 0.915493
33 UD2 0.587629 0.955882
34 UD1 0.587629 0.955882
35 USQ 0.580645 0.820513
36 UGB 0.580645 0.955224
37 UGA 0.580645 0.955224
38 UDP GAL 0.576087 0.941176
39 G3N 0.574468 0.914286
40 CJB 0.554054 0.848485
41 HWU 0.533981 0.928571
42 12V 0.533981 0.928571
43 EPZ 0.53271 0.942029
44 HP7 0.529412 0.941176
45 UD7 0.529412 0.927536
46 APU 0.527778 0.853333
47 EEB 0.527778 0.928571
48 EPU 0.527778 0.928571
49 MJZ 0.524272 0.914286
50 UD4 0.519231 0.914286
51 UDZ 0.514019 0.853333
52 U2P 0.5125 0.925373
53 IUG 0.509434 0.810127
54 U U U U 0.5 0.940298
55 UP5 0.5 0.853333
56 UMA 0.491379 0.942029
57 4TC 0.490909 0.831169
58 A U 0.486486 0.853333
59 U2G 0.482143 0.822785
60 U4S 0.481928 0.753425
61 UTP U U U 0.479167 0.924242
62 UPA 0.477477 0.866667
63 CH 0.47619 0.885714
64 DKX 0.475 0.771429
65 U3S 0.470588 0.777778
66 U2S 0.470588 0.791667
67 UMF 0.46988 0.857143
68 U20 0.467213 0.833333
69 U22 0.467213 0.8125
70 U21 0.467213 0.833333
71 UCG 0.455285 0.797468
72 U A A U 0.451613 0.842105
73 C5G 0.445545 0.915493
74 CDP 0.444444 0.887324
75 2TU 0.443038 0.774648
76 U1S 0.442105 0.773333
77 2QR 0.436508 0.822785
78 A U C C 0.434109 0.831169
79 GPC 0.433333 0.792683
80 UAG 0.431818 0.890411
81 5FU 0.430233 0.887324
82 CTP 0.430108 0.887324
83 5GW 0.418367 0.914286
84 DUD 0.417582 0.859155
85 DUT 0.414894 0.859155
86 4RA 0.413534 0.831169
87 2GW 0.412844 0.928571
88 UUA 0.4125 0.746269
89 7XL 0.412371 0.888889
90 A G U 0.410448 0.8
91 C5P 0.409091 0.9
92 C 0.409091 0.9
93 UMP 0.409091 0.871429
94 CAR 0.409091 0.9
95 DU 0.409091 0.871429
96 UD0 0.407407 0.820513
97 5BU 0.404494 0.887324
98 G U34 0.403361 0.8
99 N3E 0.402174 0.780822
100 UC5 0.402174 0.847222
101 PMP UD1 0.401515 0.818182
102 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: 64
This union binding pocket(no: 1) in the query (biounit: 5w0n.bio3) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4P 0SB 0.04043 0.42411 2.1978
2 1YKD CMP 0.009557 0.41999 2.26131
3 3KA2 2NC 0.006533 0.46444 2.46305
4 1ZAP A70 0.03206 0.4079 2.63158
5 5W4W 9WG 0.03121 0.40853 2.71903
6 2OVD DAO 0.00597 0.4178 2.74725
7 4TWL ASC 0.009249 0.40666 2.84553
8 1FMB HYB 0.03832 0.40822 2.88462
9 5XDT ZI7 0.03604 0.4027 2.92208
10 4A4X JUP 0.03808 0.40011 2.97767
11 5CFT 51G 0.02854 0.40246 3.24324
12 1ODM ASV 0.03301 0.40205 3.32326
13 1I06 TZL 0.01192 0.40129 3.33333
14 2VOT NHV 0.01253 0.40995 3.47395
15 4OIT BMA 0.01641 0.40364 3.53982
16 5IH9 6BF 0.04342 0.40629 3.58209
17 1Q23 FUA 0.02585 0.4015 3.65297
18 2PYW ADP 0.02355 0.4036 3.72208
19 4MNS 2AX 0.03179 0.4244 3.77358
20 5AIG VPR 0.0004697 0.44779 4
21 5ML3 DL3 0.0331 0.41475 4.02685
22 4D4U FUC NDG GAL FUC 0.001063 0.45411 4.12698
23 3WV6 GAL BGC 0.004783 0.42424 4.39189
24 2D6M LBT 0.007438 0.40851 4.40252
25 2AMT GPP 0.0259 0.40899 5.03145
26 4NJS G08 0.004406 0.45641 5.05051
27 4NPT 017 0.0423 0.40372 5.05051
28 5H9Q TD2 0.00342 0.42501 5.16129
29 4Q0L V14 0.01048 0.42821 5.32319
30 4OMJ 2TX 0.009029 0.43978 5.39568
31 3SAO NKN 0.005394 0.42348 5.625
32 2YG2 S1P 0.02466 0.40578 5.81395
33 4XV1 904 0.03017 0.4128 5.82192
34 1Y7P RIP 0.002847 0.43483 5.8296
35 1U0A BGC BGC BGC BGC 0.02035 0.40138 6.07477
36 4ZSI GLP 0.01928 0.40257 6.43275
37 4ZSI 4R1 0.02153 0.40014 6.43275
38 3W8X FAD 0.02475 0.4289 6.45161
39 5DG2 GAL GLC 0.001525 0.4511 6.66667
40 2YMZ LAT 0.003613 0.41364 6.92308
41 4WVW SLT 0.01327 0.4014 6.94444
42 3ZW2 GLA NAG GAL FUC 0.008993 0.42133 8.04598
43 5I8T LAC 0.003317 0.42829 8.37989
44 2R0H CTO 0.001278 0.43895 8.53659
45 2CM4 RCL 0.01302 0.41855 9.33333
46 1SIV PSI 0.006682 0.448 10.101
47 1Q79 3AT 0.0001009 0.51161 10.9181
48 1A78 TDG 0.006922 0.42146 11.194
49 1Z0N BCD 0.01617 0.40174 11.4583
50 6FIV 3TL 0.0437 0.40713 11.5044
51 1EPB REA 0.000863 0.40929 11.5854
52 4XIZ LPP 0.03742 0.40772 11.7647
53 3L9R L9Q 0.02821 0.41546 12.2449
54 3L9R L9R 0.03759 0.41171 12.2449
55 1DZK PRZ 0.002263 0.4078 12.7389
56 4HN1 TYD 0.01656 0.40386 13.9303
57 4PSB GA3 0.01873 0.4251 14.1935
58 1KJ1 MAN 0.007611 0.40245 16.5138
59 4XBT 3ZQ 0.000505 0.41259 16.7742
60 4XBT FLC 0.0005588 0.41128 16.7742
61 3GGU 017 0.002615 0.46429 18.1818
62 2O4N TPV 0.01632 0.41958 18.1818
63 2BOS GLA GAL GLC 0.0121 0.40994 19.1176
64 5K2M ADP 0.0242 0.40771 20.7547
Pocket No.: 2; Query (leader) PDB : 5W0N; Ligand: 2KH; Similar sites found: 27
This union binding pocket(no: 2) in the query (biounit: 5w0n.bio3) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5VE5 GSH 0.01338 0.4052 1.06101
2 4UP4 GAL NAG 0.0141 0.41268 1.99501
3 4U03 GTP 0.000033 0.43362 2.48139
4 5G3U FDA 0.01522 0.41563 2.48139
5 4JBL MET 0.01277 0.41162 2.65487
6 3ZNN 4WL 0.02893 0.41519 2.88184
7 3ZNN FAD 0.02893 0.41519 2.88184
8 4XJ6 GH3 0.00001609 0.5201 5.21092
9 2CDU FAD 0.02022 0.40763 5.45906
10 1KNY APC 0.0004364 0.46171 5.5336
11 3ER9 3AT 0.000762 0.44591 5.72391
12 2WET FAD 0.02448 0.40828 6.69975
13 4BC5 5FX 0.02071 0.40074 6.69975
14 4X7Y SAH 0.02564 0.40728 6.93431
15 3JZ0 APC 0.0009871 0.42945 6.96864
16 3JYY PPV 0.0006438 0.48071 8.01394
17 3B0X DGT 0.01279 0.40283 8.933
18 4CPB GAL CN8 0.01767 0.41641 10.7438
19 1Q79 3AT 0.001631 0.41875 10.9181
20 3LA3 2FT 0.01006 0.41915 11.5226
21 2B56 UTP 0.0000001168 0.63856 18.6104
22 2B56 U5P 0.0000001168 0.63856 18.6104
23 5I49 2KH 0.000005119 0.51867 22.0844
24 3HIY UTP 0.0000000002924 0.71551 36.7188
25 3HJ1 UTP 0.000000001776 0.69529 37.4677
26 5A2Z GTP 0.00000000594 0.71654 38.9578
27 4NKT 2KH 0.00000000008827 0.7365 49.2669
Pocket No.: 3; Query (leader) PDB : 5W0N; Ligand: 2KH; Similar sites found: 4
This union binding pocket(no: 3) in the query (biounit: 5w0n.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WV6 GAL GLC 0.01279 0.40125 4.39189
2 4MUQ LY0 0.01395 0.40103 5.09804
3 4MUS LY0 0.01352 0.40168 6.16114
4 3N7S 3N7 0.01744 0.40861 7.82609
Pocket No.: 4; Query (leader) PDB : 5W0N; Ligand: UPU; Similar sites found: 7
This union binding pocket(no: 4) in the query (biounit: 5w0n.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FFG 0U8 0.02767 0.4006 1.48883
2 3NW7 LGV 0.02747 0.40447 2.60586
3 2UVF AD0 0.01585 0.40031 3.47395
4 5L4S NAP 0.02471 0.4013 4.71698
5 5L4S 6KX 0.02471 0.4013 4.71698
6 3KFF XBT 0.02333 0.40027 5.55556
7 3KFF ZBT 0.02333 0.40027 5.55556
Pocket No.: 5; Query (leader) PDB : 5W0N; Ligand: 2KH; Similar sites found: 4
This union binding pocket(no: 5) in the query (biounit: 5w0n.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ICS FAD 0.03183 0.40306 2.21088
2 2Z3Y F2N 0.04042 0.40214 6.45161
3 3KRB NAP 0.01473 0.40976 13.4731
4 2XKO AKG 0.01651 0.40556 23.5955
Pocket No.: 6; Query (leader) PDB : 5W0N; Ligand: UPU; Similar sites found: 3
This union binding pocket(no: 6) in the query (biounit: 5w0n.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TKB N1T 0.0155 0.41457 6.20347
2 2GJ5 VD3 0.03199 0.40105 9.87654
3 3T3C 017 0.0112 0.4142 13.1313
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