Receptor
PDB id Resolution Class Description Source Keywords
4NES 1.42 Å EC: 5.1.3.14 CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII UDP-GLCNA EPIMERASE IN COMPLEX WITH UDP-GLCNAC AND UDP METHANOCALDOCOCCUS JANNASCHII UDP-GLYCOSYLTRANSFERASE/GLYCOGEN PHOSPHORYLASE FOLD UDP-GLCEPIMERASE ISOMERASE
Ref.: CRYSTAL STRUCTURES OF THE ARCHAEAL UDP-GLCNAC 2-EPI FROM METHANOCALDOCOCCUS JANNASCHII REVEAL A CONFORM CHANGE INDUCED BY UDP-GLCNAC. PROTEINS V. 82 1519 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UD1 A:400;
Valid;
none;
submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
UDP A:401;
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
4NES 1.42 Å EC: 5.1.3.14 CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII UDP-GLCNA EPIMERASE IN COMPLEX WITH UDP-GLCNAC AND UDP METHANOCALDOCOCCUS JANNASCHII UDP-GLYCOSYLTRANSFERASE/GLYCOGEN PHOSPHORYLASE FOLD UDP-GLCEPIMERASE ISOMERASE
Ref.: CRYSTAL STRUCTURES OF THE ARCHAEAL UDP-GLCNAC 2-EPI FROM METHANOCALDOCOCCUS JANNASCHII REVEAL A CONFORM CHANGE INDUCED BY UDP-GLCNAC. PROTEINS V. 82 1519 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4NES - UDP C9 H14 N2 O12 P2 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 5 families.
1 4NES - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ENZ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 3BEO - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 6VLC - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
4 4NES - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: UD1; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 UD2 1 1
2 UD1 1 1
3 UDZ 0.8 0.893333
4 HP7 0.793814 0.985294
5 EPZ 0.75 0.985507
6 EEB 0.742857 0.971429
7 EPU 0.742857 0.971429
8 F5P 0.742574 0.957143
9 F5G 0.742574 0.971014
10 UD4 0.742574 0.957143
11 UPG 0.73913 0.985294
12 GDU 0.73913 0.985294
13 UFM 0.73913 0.985294
14 UD7 0.722772 0.971014
15 MJZ 0.715686 0.957143
16 UPF 0.697917 0.930556
17 U2F 0.697917 0.930556
18 UMA 0.690265 0.985507
19 UDM 0.683168 0.957143
20 UFG 0.663265 0.930556
21 HWU 0.660377 0.943662
22 12V 0.660377 0.943662
23 AWU 0.659794 0.985294
24 U20 0.655462 0.871795
25 U21 0.655462 0.871795
26 U22 0.655462 0.85
27 UGA 0.65 0.970588
28 UGB 0.65 0.970588
29 USQ 0.633663 0.835443
30 UAD 0.63 0.956522
31 UDX 0.63 0.956522
32 UGF 0.627451 0.916667
33 UDP 0.622222 0.927536
34 UTP 0.619565 0.927536
35 UAG 0.617188 0.931507
36 U5F 0.612903 0.927536
37 URM 0.6 0.942857
38 660 0.6 0.942857
39 G3N 0.596154 0.929577
40 UPU 0.587629 0.955882
41 4RA 0.584615 0.87013
42 UNP 0.583333 0.901408
43 3UC 0.575472 0.930556
44 UML 0.564286 0.871795
45 IUG 0.561404 0.825
46 U5P 0.555556 0.913043
47 U 0.555556 0.913043
48 UDP GAL 0.552381 0.956522
49 UD0 0.552239 0.858974
50 UPP 0.543689 0.928571
51 UDH 0.543689 0.855263
52 2KH 0.530612 0.901408
53 44P 0.521277 0.888889
54 C5G 0.518519 0.930556
55 UDP UDP 0.505155 0.898551
56 Y6W 0.504673 0.90411
57 2QR 0.485075 0.860759
58 2GW 0.482759 0.943662
59 URI 0.477273 0.852941
60 UP5 0.47541 0.844156
61 PMP UD1 0.467626 0.848101
62 1GW 0.467213 0.905405
63 CJB 0.461538 0.838235
64 UAG API 0.457516 0.87013
65 4TC 0.456 0.822785
66 CSQ 0.452991 0.866667
67 CSV 0.452991 0.866667
68 U3P 0.447917 0.898551
69 UA3 0.447917 0.898551
70 GN1 0.444444 0.753623
71 NG1 0.444444 0.753623
72 C30 0.433628 0.696203
73 Q5S 0.433628 0.696203
74 FZK 0.431193 0.771084
75 PUP 0.429825 0.875
76 LSU 0.428571 0.732558
77 CXY 0.422414 0.90411
78 U2P 0.418367 0.913043
79 UMA FGA LYS DAL DAL 0.414634 0.8375
80 U1S 0.409091 0.789474
81 FN5 0.40458 0.883117
82 YSU 0.403361 0.741176
83 DAU 0.403361 0.905405
Ligand no: 2; Ligand: UDP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 U5F 0.878788 1
4 UNP 0.8 0.970149
5 U5P 0.78125 0.984615
6 U 0.78125 0.984615
7 UPU 0.72973 0.940298
8 2KH 0.722222 0.970149
9 44P 0.720588 0.955882
10 UFM 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GDU 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UDH 0.705128 0.864865
17 UPP 0.705128 0.941176
18 UFG 0.691358 0.888889
19 U2F 0.691358 0.888889
20 UPF 0.691358 0.888889
21 AWU 0.6875 0.941176
22 UAD 0.670732 0.941176
23 UDX 0.670732 0.941176
24 3UC 0.658824 0.888889
25 UGA 0.654762 0.955224
26 UGB 0.654762 0.955224
27 USQ 0.654762 0.820513
28 G3N 0.647059 0.914286
29 UGF 0.647059 0.901408
30 UDM 0.636364 0.914286
31 URI 0.625 0.863636
32 UD1 0.622222 0.927536
33 UD2 0.622222 0.927536
34 UDP GAL 0.611765 0.913043
35 Y6W 0.607143 0.888889
36 CDP 0.605263 0.942029
37 HP7 0.591398 0.941176
38 UD7 0.591398 0.927536
39 MJZ 0.585106 0.914286
40 IUG 0.583333 0.810127
41 HWU 0.578947 0.901408
42 UD4 0.578947 0.914286
43 12V 0.578947 0.901408
44 F5G 0.578947 0.927536
45 F5P 0.578947 0.914286
46 CJB 0.573529 0.820895
47 UDZ 0.571429 0.853333
48 DUD 0.571429 0.913043
49 UP5 0.571429 0.853333
50 EPZ 0.56 0.914286
51 5GW 0.559524 0.942029
52 EEB 0.554455 0.901408
53 EPU 0.554455 0.901408
54 UA3 0.547945 0.939394
55 U3P 0.547945 0.939394
56 4TC 0.544554 0.831169
57 HF4 0.54321 0.942029
58 CTP 0.54321 0.942029
59 BUP 0.536585 0.928571
60 CSV 0.531915 0.851351
61 CSQ 0.531915 0.851351
62 DUT 0.52439 0.913043
63 4GW 0.516484 0.915493
64 UMA 0.513761 0.914286
65 U4S 0.513158 0.753425
66 U2P 0.506667 0.954545
67 U3S 0.5 0.753425
68 U2S 0.5 0.767123
69 FZK 0.494253 0.777778
70 PUP 0.48913 0.913043
71 U21 0.486957 0.810127
72 U20 0.486957 0.810127
73 U22 0.486957 0.790123
74 DKX 0.486486 0.746479
75 U1S 0.482759 0.75
76 0RC 0.482759 0.864865
77 2QR 0.478632 0.822785
78 5FU 0.474359 0.914286
79 LSU 0.472527 0.738095
80 8OD 0.47191 0.851351
81 C5G 0.468085 0.888889
82 7XL 0.465909 0.888889
83 UMF 0.461538 0.857143
84 G8D 0.460674 0.855263
85 2TM 0.45977 0.902778
86 UTP U U U 0.456522 0.895522
87 YSU 0.453608 0.746988
88 2TU 0.452055 0.774648
89 4RA 0.451613 0.855263
90 C2G 0.450549 0.901408
91 DU 0.45 0.898551
92 CAR 0.45 0.927536
93 UMP 0.45 0.898551
94 C5P 0.45 0.927536
95 C 0.45 0.927536
96 UAG 0.448 0.864865
97 CDC 0.446809 0.777778
98 5BU 0.444444 0.914286
99 UD0 0.444444 0.844156
100 N3E 0.440476 0.733333
101 UC5 0.440476 0.9
102 UUA 0.438356 0.772727
103 DUP 0.431818 0.887324
104 2GW 0.431373 0.901408
105 M7G 0.430108 0.780488
106 CNU 0.428571 0.927536
107 CDM 0.427083 0.842105
108 H6Y 0.425532 0.851351
109 16B 0.421687 0.888889
110 S5P 0.419753 0.915493
111 8GT 0.419355 0.855263
112 CDP MG 0.418605 0.885714
113 CXY 0.418367 0.888889
114 UPA 0.418182 0.842105
115 U2G 0.410714 0.822785
116 UML 0.408759 0.810127
117 UP6 0.407407 0.871429
118 M7M 0.40625 0.771084
119 1GW 0.40367 0.864865
120 BMP 0.402439 0.970149
121 APU 0.401786 0.828947
122 PMP UD1 0.401575 0.7875
123 DUT MG 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: UD1; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GDD 0.8671
2 TDX 0.8645
Ligand no: 2; Ligand: UDP; Similar ligands found: 55
No: Ligand Similarity coefficient
1 YYY 0.9739
2 TYD 0.9699
3 TBD 0.9623
4 GCQ 0.9509
5 ADP 0.9410
6 DUN 0.9317
7 D4D 0.9237
8 ADX 0.9224
9 AU1 0.9218
10 AP2 0.9215
11 SON 0.9211
12 GDP 0.9193
13 DAT 0.9189
14 IDP 0.9155
15 PRX 0.9148
16 ADP MG 0.9122
17 BEF ADP 0.9122
18 AN2 0.9115
19 A12 0.9102
20 M33 0.9098
21 CA0 0.9083
22 G5A 0.9077
23 CUU 0.9055
24 GAP 0.8984
25 DGI 0.8977
26 GNH 0.8961
27 FZQ 0.8919
28 7D3 0.8915
29 DAL AMP 0.8905
30 H2U 0.8888
31 CH 0.8874
32 AZD 0.8849
33 PSU 0.8815
34 CK7 0.8802
35 AMP 0.8793
36 FN5 0.8781
37 6AD 0.8757
38 A5A 0.8754
39 HQ5 0.8747
40 DCM 0.8724
41 8LH 0.8718
42 8GD 0.8708
43 ATY 0.8691
44 BMQ 0.8679
45 U6M 0.8672
46 NUP 0.8671
47 DC 0.8658
48 DCP 0.8657
49 TMP 0.8642
50 C8M 0.8633
51 TTP 0.8581
52 ATP 0.8570
53 DDN 0.8568
54 C2R 0.8549
55 D4T 0.8531
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NES; Ligand: UDP; 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: 4nes.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4NES; Ligand: UDP; 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: 4nes.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4NES; Ligand: UD1; 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: 4nes.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4NES; Ligand: UD1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4nes.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback