Receptor
PDB id Resolution Class Description Source Keywords
1NVK 1.8 Å EC: 2.4.1.27 T4 PHAGE BGT IN COMPLEX WITH UDP AND A MN2+ ION AT 1.8 A RES ENTEROBACTERIA PHAGE T4 GLYCOSYLTRANSFERASE GT-B MN TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF THE T4 PHAGE BETA-GLUCOSYLTRA AND THE D100A MUTANT IN COMPLEX WITH UDP-GLUCOSE: G BINDING AND IDENTIFICATION OF THE CATALYTIC BASE FO DIRECT DISPLACEMENT MECHANISM J.MOL.BIOL. V. 330 1077 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:702;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MN A:701;
Invalid;
none;
submit data
54.938 Mn [Mn+2...
UDP A:700;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1J39 1.87 Å EC: 2.4.1.27 CRYSTAL STRUCTURE OF T4 PHAGE BGT IN COMPLEX WITH ITS UDP-GL SUBSTRATE ENTEROBACTERIA PHAGE T4 GLYCOSYLTRANSFERASE GT-B UDP-GLUCOSE TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF THE T4 PHAGE BETA-GLUCOSYLTRA AND THE D100A MUTANT IN COMPLEX WITH UDP-GLUCOSE: G BINDING AND IDENTIFICATION OF THE CATALYTIC BASE FO DIRECT DISPLACEMENT MECHANISM. J.MOL.BIOL. V. 330 1077 2003
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1JG7 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 1JG6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 1J39 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
4 1BGU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 1NVK - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 1JIX - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 1NZD - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
8 1QKJ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 1JIV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
10 2BGU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
11 1C3J - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 1JIU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
13 1NZF - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1JG7 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 1JG6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 1J39 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
4 1BGU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 1NVK - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 1JIX - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 1NZD - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
8 1QKJ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 1JIV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
10 2BGU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
11 1C3J - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 1JIU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
13 1NZF - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1JG7 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 1JG6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 1J39 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
4 1BGU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 1NVK - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 1JIX - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 1NZD - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
8 1QKJ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 1JIV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
10 2BGU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
11 1C3J - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 1JIU - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
13 1NZF - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UDP; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U 0.78125 0.984615
5 U5P 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 GUD 0.717949 0.941176
10 UFM 0.717949 0.941176
11 GDU 0.717949 0.941176
12 UPG 0.717949 0.941176
13 UDP UDP 0.714286 0.939394
14 UPP 0.705128 0.941176
15 UDH 0.705128 0.864865
16 UPF 0.691358 0.888889
17 U2F 0.691358 0.888889
18 UFG 0.691358 0.888889
19 UDX 0.670732 0.941176
20 UAD 0.670732 0.941176
21 USQ 0.654762 0.820513
22 UGB 0.654762 0.955224
23 UGA 0.654762 0.955224
24 UDM 0.636364 0.914286
25 URI 0.625 0.863636
26 UD1 0.622222 0.927536
27 UD2 0.622222 0.927536
28 UDP GAL 0.611765 0.913043
29 CDP 0.605263 0.942029
30 HP7 0.591398 0.941176
31 UD7 0.591398 0.927536
32 MJZ 0.585106 0.914286
33 IUG 0.583333 0.810127
34 12V 0.578947 0.901408
35 UD4 0.578947 0.914286
36 HWU 0.578947 0.901408
37 CJB 0.573529 0.820895
38 DUD 0.571429 0.913043
39 UDZ 0.571429 0.853333
40 UP5 0.571429 0.853333
41 U U 0.563218 0.955224
42 EPZ 0.56 0.914286
43 5GW 0.559524 0.942029
44 EPU 0.554455 0.901408
45 EEB 0.554455 0.901408
46 UA3 0.547945 0.939394
47 U3P 0.547945 0.939394
48 4TC 0.544554 0.831169
49 CTP 0.54321 0.942029
50 CSQ 0.531915 0.851351
51 CSV 0.531915 0.851351
52 DUT 0.52439 0.913043
53 4GW 0.516484 0.915493
54 UMA 0.513761 0.914286
55 U4S 0.513158 0.753425
56 U2P 0.506667 0.954545
57 U2S 0.5 0.767123
58 U3S 0.5 0.753425
59 PUP 0.48913 0.913043
60 U21 0.486957 0.810127
61 U20 0.486957 0.810127
62 U22 0.486957 0.790123
63 DKX 0.486486 0.746479
64 U1S 0.482759 0.75
65 A U 0.481132 0.805195
66 2QR 0.478632 0.822785
67 5FU 0.474359 0.914286
68 8OD 0.47191 0.851351
69 C5G 0.468085 0.888889
70 UMF 0.461538 0.857143
71 UTP U U U 0.456522 0.895522
72 2TU 0.452055 0.774648
73 C2G 0.450549 0.901408
74 CAR 0.45 0.927536
75 C 0.45 0.927536
76 UMP 0.45 0.898551
77 DU 0.45 0.898551
78 C5P 0.45 0.927536
79 UAG 0.448 0.864865
80 CDC 0.446809 0.777778
81 UD0 0.444444 0.844156
82 5BU 0.444444 0.914286
83 N3E 0.440476 0.733333
84 UC5 0.440476 0.9
85 DUP 0.431818 0.887324
86 2GW 0.431373 0.901408
87 M7G 0.430108 0.780488
88 CNU 0.428571 0.927536
89 CDM 0.427083 0.842105
90 16B 0.421687 0.888889
91 S5P 0.419753 0.915493
92 8GT 0.419355 0.855263
93 CXY 0.418367 0.888889
94 UPA 0.418182 0.842105
95 CDP MG 0.413793 0.849315
96 U2G 0.410714 0.822785
97 UML 0.408759 0.810127
98 UP6 0.407407 0.871429
99 M7M 0.40625 0.771084
100 PMP UD1 0.404762 0.794872
101 1GW 0.40367 0.864865
102 BMP 0.402439 0.970149
103 APU 0.401786 0.828947
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1J39; Ligand: UPG; Similar sites found: 48
This union binding pocket(no: 1) in the query (biounit: 1j39.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 3CV3 UDP 3.206e-05 0.52355
2 3RHZ UDP 0.0001169 0.49274
3 3OKP GDD 0.000392 0.48383
4 4PQG UDP 0.0003082 0.46938
5 4PQG UDP 0.0003194 0.4687
6 1RZU ADP 0.001773 0.4622
7 1RZU ADP 0.003114 0.44525
8 4EE7 PIS 0.007361 0.43957
9 3B6R CRN 0.01479 0.43504
10 3Q3H UDP 0.006946 0.43248
11 2IW1 U2F 0.001231 0.42241
12 4I9B 1KA 0.03147 0.41974
13 2IV3 UDP 0.0002273 0.41883
14 2ZWS PLM 0.006159 0.41839
15 2ZWS PLM 0.006159 0.41839
16 3OTI TYD 0.004199 0.41624
17 3OTI TYD 0.004199 0.41624
18 2IV3 UDP 0.0003021 0.41521
19 3Q3H UDP 0.02592 0.41161
20 3AIA SAM 0.01125 0.4105
21 1GPM AMP 0.02795 0.40885
22 3UPY FOM 0.02753 0.40736
23 2WTX VDO 0.004624 0.40727
24 2WTX UDP 0.004332 0.40727
25 4KBC 1QJ 0.01856 0.4072
26 3UZO PLP 0.01882 0.40691
27 3BBH SFG 0.01196 0.40586
28 1Y8E SVR 0.03551 0.40544
29 4HNN LYS 0.03345 0.40476
30 3HT5 PMP 0.01762 0.40473
31 4N39 UDP 0.01513 0.40444
32 4CLJ 5P8 0.016 0.40331
33 1SZO CAX 0.03962 0.40321
34 1SZO CAX 0.03969 0.40304
35 1SZO CAX 0.03969 0.40304
36 3AJ6 NGA 0.03832 0.40287
37 3AJ6 NGA 0.03832 0.40287
38 4HNN LYS 0.04046 0.40242
39 2H1H AFH 0.008851 0.40227
40 1XV5 UDP 0.01691 0.40217
41 4KBC 1QJ 0.02368 0.40198
42 4KBC 1QJ 0.02368 0.40198
43 4KBA 1QM 0.0241 0.4016
44 2XA2 UPG 0.01085 0.40143
45 3RET PYR 0.02089 0.40116
46 3RET SAL 0.02089 0.40116
47 4UYG 73B 0.04599 0.40072
48 1TVP CBI 0.03113 0.40068
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