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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 5 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 4 families.
1 4NES - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (3)
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 4NES - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UD1; Similar ligands found: 79
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 EPU 0.742857 0.971429
7 EEB 0.742857 0.971429
8 F5P 0.742574 0.957143
9 UD4 0.742574 0.957143
10 F5G 0.742574 0.971014
11 UFM 0.73913 0.985294
12 GUD 0.73913 0.985294
13 UPG 0.73913 0.985294
14 GDU 0.73913 0.985294
15 UD7 0.722772 0.971014
16 MJZ 0.715686 0.957143
17 U2F 0.697917 0.930556
18 UPF 0.697917 0.930556
19 UMA 0.690265 0.985507
20 UDM 0.683168 0.957143
21 UFG 0.663265 0.930556
22 12V 0.660377 0.943662
23 HWU 0.660377 0.943662
24 U22 0.655462 0.85
25 U20 0.655462 0.871795
26 U21 0.655462 0.871795
27 UGB 0.65 0.970588
28 UGA 0.65 0.970588
29 USQ 0.633663 0.835443
30 UDX 0.63 0.956522
31 UAD 0.63 0.956522
32 UDP 0.622222 0.927536
33 UTP 0.619565 0.927536
34 UAG 0.617188 0.931507
35 660 0.6 0.942857
36 URM 0.6 0.942857
37 G3N 0.596154 0.929577
38 UPU 0.587629 0.955882
39 4RA 0.584615 0.87013
40 UNP 0.583333 0.901408
41 3UC 0.575472 0.930556
42 UML 0.564286 0.871795
43 IUG 0.561404 0.825
44 U5P 0.555556 0.913043
45 U 0.555556 0.913043
46 UD0 0.552239 0.858974
47 UPP 0.543689 0.928571
48 UDH 0.543689 0.855263
49 2KH 0.530612 0.901408
50 44P 0.521277 0.888889
51 C5G 0.518519 0.930556
52 UDP UDP 0.505155 0.898551
53 Y6W 0.504673 0.90411
54 2QR 0.485075 0.860759
55 2GW 0.482759 0.943662
56 URI 0.477273 0.852941
57 UP5 0.47541 0.844156
58 PMP UD1 0.467626 0.848101
59 1GW 0.467213 0.905405
60 CJB 0.461538 0.838235
61 UAG API 0.457516 0.87013
62 4TC 0.456 0.822785
63 CSV 0.452991 0.866667
64 CSQ 0.452991 0.866667
65 U3P 0.447917 0.898551
66 UA3 0.447917 0.898551
67 U U 0.446429 0.914286
68 NG1 0.444444 0.753623
69 GN1 0.444444 0.753623
70 C30 0.433628 0.696203
71 PUP 0.429825 0.875
72 CXY 0.422414 0.90411
73 A U 0.418605 0.820513
74 U2P 0.418367 0.913043
75 UMA FGA LYS DAL DAL 0.414634 0.8375
76 U1S 0.409091 0.789474
77 FN5 0.40458 0.883117
78 DAU 0.403361 0.905405
79 G U 0.401515 0.780488
Ligand no: 2; Ligand: UDP; Similar ligands found: 117
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
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: 89
This union binding pocket(no: 1) in the query (biounit: 4nes.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 2XRH NIO None
3 1ZEI CRS None
4 3WJO IPE 1.48368
5 2VDY HCY 1.87668
6 4WBD CIT 2.13904
7 5XVR TRH 2.13904
8 2WTX UDP 2.13904
9 5CX8 RP3 2.13904
10 2WTX VDO 2.13904
11 4CNK FAD 2.13904
12 2IV3 UDP 2.33918
13 1DUV PSQ 2.4024
14 4GYW UDP 2.40642
15 5BNW 12V 2.40642
16 4N3A UDP 2.40642
17 5UY8 AMZ 2.40642
18 5A1S FLC 2.40642
19 6EJI UD2 2.41287
20 4Z87 GDP 2.6738
21 2IW1 U2F 2.6738
22 1NP7 FAD 2.6738
23 4YZC STU 2.6738
24 2AL2 PEP 2.6738
25 2GEK GDP 2.94118
26 3OKP GDD 3.20856
27 4I6G FAD 3.20856
28 4WNK 453 3.20856
29 2RH4 EMO 3.2491
30 1MID LAP 3.2967
31 1U08 PLP 3.47594
32 5CKS GAL 3.47594
33 4F97 GDP 3.47594
34 1XQP 8HG 3.51562
35 5NDB 8TW 3.6
36 4RW3 DKA 3.64238
37 3P9T TCL 3.65297
38 4ORM ORO 3.74332
39 4ORM FMN 3.74332
40 4ORM 2V6 3.74332
41 4GU5 FAD 3.74332
42 5VEQ PMP 3.74332
43 4DDY DN6 3.80228
44 3B8I OXL 4.18118
45 3BF8 MLA 4.31373
46 4P8K 38C 4.375
47 4P8K FAD 4.375
48 1UU1 PMP HSA 4.54545
49 6CZY PMP 4.69613
50 2ARC ARA 4.87805
51 4G86 BNT 4.92958
52 3Q3H UDP 5.08021
53 4KVL PLM 5.08021
54 3LA3 2FT 5.34979
55 1HBK MYR 5.61798
56 2CJF RP4 5.73248
57 2JLB UDM 5.88235
58 3K60 ADP 6.14973
59 5OF1 SAL 6.19048
60 5ZM0 FAD 6.68449
61 1QF9 ALF 6.70103
62 1QF9 ADP 6.70103
63 1QF9 C5P 6.70103
64 1VR0 3SL 6.88259
65 3CV3 UDP 7.21925
66 3KP6 SAL 7.28477
67 3ITJ CIT 7.39645
68 5LX9 OLB 7.49186
69 3B6C SDN 7.69231
70 5A0U CHT 7.75401
71 4CUB GAL NAG 8.19672
72 5W6Y TRP 8.22785
73 3RSC TYD 8.55615
74 3IAA TYD 8.55615
75 5WXK TYD 8.57143
76 3N8K D1X 9.30233
77 4XSU UDP 9.89305
78 4XSU GLC 9.89305
79 2JKG PRO PRO PRO PRO PRO PRO PRO PRO 10.0559
80 4PQG UDP 11.2299
81 1T0S BML 11.6279
82 5HZ9 5M8 11.8519
83 3OKA GDD 14.2857
84 2AE2 PTO 15.7692
85 2AE2 NAP 15.7692
86 4K7O EKZ 16.0714
87 5NV8 TRH 16.5775
88 3F8C HT1 23.0159
89 5XVS UDP 44.385
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: 24
This union binding pocket(no: 3) in the query (biounit: 4nes.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2XMY CDK 2.01342
2 3HUN ZZ7 2.13904
3 4XF6 LIP 2.9304
4 4XF6 ADP 2.9304
5 4XF6 INS 2.9304
6 3WRB GDE 2.94118
7 5TPC GAL SIA NGA GAL SIA 3.47594
8 2JBM SRT 3.67893
9 3JQM GTP 4.4586
10 4AVV GHE 4.90196
11 4AVV CD 4.90196
12 3PCJ INO 5
13 1K4M CIT 5.6338
14 5ZI9 FLC 6.15385
15 3E8N ATP 7.03812
16 3E8N VRA 7.03812
17 5IUC SIA GAL A2G 7.08661
18 5EI3 5O8 7.37327
19 3FYP PEP 7.5
20 3UVD MB3 9.67742
21 3PMA SCR 10.3448
22 3IWD M2T 11.7647
23 1K1Y MAL 13.9037
24 1DCP HBI 21.1538
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
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