Receptor
PDB id Resolution Class Description Source Keywords
3U2U 1.45 Å EC: 2.4.1.186 CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WIT MANGANESE, UDP AND MALTOTETRAOSE HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC TRANSFERASE GLYCOSYLTRANSFERASE GLYCOGEN BIOSYNTHESIS GLYCOSYLATION OLIGOSACCHARIDE SUGAR CHAIN RETAINING ANOMCONFIGURATION
Ref.: CONFORMATIONAL PLASTICITY OF GLYCOGENIN AND ITS MALTOSACCHARIDE SUBSTRATE DURING GLYCOGEN BIOGENESI PROC.NATL.ACAD.SCI.USA V. 108 21028 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLC GLC GLC GLC A:263;
B:263;
Invalid;
Invalid;
none;
none;
submit data
666.579 n/a O(C1O...
GOL A:269;
A:270;
B:270;
B:271;
B:272;
B:273;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MN A:267;
B:267;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
SO4 B:269;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
UDP A:268;
B:268;
Valid;
Valid;
none;
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
3U2U 1.45 Å EC: 2.4.1.186 CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WIT MANGANESE, UDP AND MALTOTETRAOSE HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC TRANSFERASE GLYCOSYLTRANSFERASE GLYCOGEN BIOSYNTHESIS GLYCOSYLATION OLIGOSACCHARIDE SUGAR CHAIN RETAINING ANOMCONFIGURATION
Ref.: CONFORMATIONAL PLASTICITY OF GLYCOGENIN AND ITS MALTOSACCHARIDE SUBSTRATE DURING GLYCOGEN BIOGENESI PROC.NATL.ACAD.SCI.USA V. 108 21028 2011
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3U2V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 3QVB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 3T7M - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
4 3U2W - LCN C6 H10 O5 C1=C([C@H]....
5 3T7O - GLC C6 H12 O6 C([C@@H]1[....
6 3T7N - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 3U2U - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
8 3RMW - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
9 3RMV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3V91 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
2 3V8Z - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 3U2V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
4 3QVB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 3T7M - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3U2W - LCN C6 H10 O5 C1=C([C@H]....
7 3T7O - GLC C6 H12 O6 C([C@@H]1[....
8 3T7N - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 3U2U - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
10 3RMW - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
11 3RMV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 1ZDF - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
13 1ZDG - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
14 1LL2 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3V91 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
2 3V8Z - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 3U2V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
4 3QVB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 3T7M - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3U2W - LCN C6 H10 O5 C1=C([C@H]....
7 3T7O - GLC C6 H12 O6 C([C@@H]1[....
8 3T7N - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 3U2U - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
10 3RMW - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
11 3RMV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 1ZDF - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
13 1ZDG - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
14 1LL2 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UDP; Similar ligands found: 116
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 UPU 0.72973 0.940298
6 2KH 0.722222 0.970149
7 44P 0.720588 0.955882
8 URM 0.717949 0.927536
9 GUD 0.717949 0.941176
10 GDU 0.717949 0.941176
11 UFM 0.717949 0.941176
12 UPG 0.717949 0.941176
13 660 0.717949 0.927536
14 UDP UDP 0.714286 0.939394
15 UDH 0.705128 0.864865
16 UPP 0.705128 0.941176
17 UPF 0.691358 0.888889
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UDX 0.670732 0.941176
21 UAD 0.670732 0.941176
22 3UC 0.658824 0.888889
23 USQ 0.654762 0.820513
24 UGB 0.654762 0.955224
25 UGA 0.654762 0.955224
26 G3N 0.647059 0.914286
27 UDM 0.636364 0.914286
28 URI 0.625 0.863636
29 U 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 UDP GAL 0.611765 0.913043
33 Y6W 0.607143 0.888889
34 CDP 0.605263 0.942029
35 UD7 0.591398 0.927536
36 HP7 0.591398 0.941176
37 MJZ 0.585106 0.914286
38 IUG 0.583333 0.810127
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 UD4 0.578947 0.914286
42 CJB 0.573529 0.820895
43 UDZ 0.571429 0.853333
44 DUD 0.571429 0.913043
45 UP5 0.571429 0.853333
46 U U 0.563218 0.955224
47 EPZ 0.56 0.914286
48 5GW 0.559524 0.942029
49 EPU 0.554455 0.901408
50 EEB 0.554455 0.901408
51 UA3 0.547945 0.939394
52 U3P 0.547945 0.939394
53 CH 0.546667 0.913043
54 4TC 0.544554 0.831169
55 CTP 0.54321 0.942029
56 CSV 0.531915 0.851351
57 CSQ 0.531915 0.851351
58 DUT 0.52439 0.913043
59 4GW 0.516484 0.915493
60 UMA 0.513761 0.914286
61 U4S 0.513158 0.753425
62 U2P 0.506667 0.954545
63 U2S 0.5 0.767123
64 U3S 0.5 0.753425
65 PUP 0.48913 0.913043
66 U22 0.486957 0.790123
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 DKX 0.486486 0.746479
70 U1S 0.482759 0.75
71 A U 0.481132 0.805195
72 2QR 0.478632 0.822785
73 5FU 0.474359 0.914286
74 8OD 0.47191 0.851351
75 C5G 0.468085 0.888889
76 7XL 0.465909 0.888889
77 U U U U 0.461538 0.940298
78 UMF 0.461538 0.857143
79 G8D 0.460674 0.855263
80 UTP U U U 0.456522 0.895522
81 2TU 0.452055 0.774648
82 4RA 0.451613 0.855263
83 C2G 0.450549 0.901408
84 DU 0.45 0.898551
85 CAR 0.45 0.927536
86 C 0.45 0.927536
87 C5P 0.45 0.927536
88 UMP 0.45 0.898551
89 UAG 0.448 0.864865
90 CDC 0.446809 0.777778
91 UD0 0.444444 0.844156
92 5BU 0.444444 0.914286
93 N3E 0.440476 0.733333
94 UC5 0.440476 0.9
95 UUA 0.438356 0.772727
96 DUP 0.431818 0.887324
97 2GW 0.431373 0.901408
98 M7G 0.430108 0.780488
99 CNU 0.428571 0.927536
100 CDM 0.427083 0.842105
101 H6Y 0.425532 0.851351
102 16B 0.421687 0.888889
103 S5P 0.419753 0.915493
104 8GT 0.419355 0.855263
105 CXY 0.418367 0.888889
106 UPA 0.418182 0.842105
107 CDP MG 0.413793 0.849315
108 U2G 0.410714 0.822785
109 U A A U 0.409836 0.842105
110 UML 0.408759 0.810127
111 UP6 0.407407 0.871429
112 M7M 0.40625 0.771084
113 PMP UD1 0.404762 0.794872
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3U2U; Ligand: UDP; Similar sites found: 76
This union binding pocket(no: 1) in the query (biounit: 3u2u.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2AJH MET 0.03766 0.41068 None
2 4ZYB 4SQ 0.03941 0.40649 None
3 4M4K XYP XYP 0.0009563 0.44973 1.14068
4 4M4K GDU 0.0009563 0.44973 1.14068
5 3L6C MLI 0.009723 0.44538 1.14068
6 3O94 NCA 0.04848 0.40263 1.4218
7 3JQ7 DX2 0.03055 0.4151 1.52091
8 2XSB GDL 0.03133 0.40791 1.52091
9 3BMQ AX5 0.04057 0.40752 1.52091
10 2VL8 CTS 0.0005623 0.46818 2.28137
11 2VL8 UDP 0.0005085 0.46586 2.28137
12 2FV1 GAD NDG 0.0429 0.40067 2.28137
13 4J25 OGA 0.03644 0.40819 2.62009
14 2WZF UDP 0.003949 0.44126 2.6616
15 4MIX UD1 0.003373 0.44043 2.6616
16 2D7I UDP 0.01176 0.42198 2.6616
17 2WZF BGC 0.02889 0.41519 2.6616
18 3BP1 GUN 0.0393 0.40035 2.6616
19 4U98 ACP 0.02373 0.40001 2.6616
20 3OQJ 3CX 0.04683 0.40241 2.72374
21 2XBL M7P 0.01999 0.40359 3.0303
22 1TZJ A3B 0.01945 0.42508 3.04183
23 1FGX U5P 0.02335 0.4135 3.04183
24 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.01707 0.40687 3.04183
25 5N53 8NB 0.03355 0.41114 3.07692
26 5FV9 Y6W 0.001107 0.43977 3.80228
27 5UQK U2F 0.001209 0.43815 3.80228
28 5FV9 UDP 0.002009 0.42567 3.80228
29 5AB1 BCD TA5 HP6 MAN 0.02748 0.41437 3.80228
30 5AJP UDP 0.02039 0.40318 3.80228
31 4MBY BGC SIA GAL 0.0454 0.40314 3.80228
32 3GU3 SAH 0.03472 0.40186 3.80228
33 4R78 AMP 0.04093 0.40176 3.80228
34 2JAC GSH 0.01981 0.42192 4.54545
35 3JSZ UPG 0.002371 0.43247 4.56274
36 1E4E ADP 0.01159 0.40825 4.94297
37 2VHL GLP 0.03071 0.40461 4.94297
38 3IOI 1GW 0.0001019 0.45395 5.32319
39 3OBT SLB 0.03153 0.40215 5.32319
40 1G0H IPD 0.02046 0.4031 5.55556
41 2P6W FLC 0.00001135 0.41074 5.6338
42 2BVL GLC 0.0008442 0.44473 5.70342
43 2BVL UDP 0.0008442 0.44473 5.70342
44 5GQX GLC GLC GLC GLC 0.01423 0.4233 5.70342
45 4L6H HCS 0.0338 0.41116 5.70342
46 2Z9V PXM 0.03601 0.40863 5.70342
47 4XBA GMP 0.01812 0.4126 6
48 2QGI UDP 0.005451 0.45384 6.04839
49 2OVW CBI 0.01145 0.43088 6.08365
50 3S6X SIA GAL BGC 0.042 0.40671 6.08365
51 1OJJ GLC GAL 0.007565 0.44029 6.46388
52 4A3R CIT 0.007299 0.42828 6.46388
53 2C91 TLA 0.03947 0.40005 6.80473
54 3X27 TRP 0.02074 0.41735 6.84411
55 1AF6 GLC FRU 0.02921 0.4151 6.84411
56 3NOJ PYR 0.02768 0.41442 7.14286
57 5X20 AOT 0.01831 0.42648 7.22433
58 4IRP UDP 0.002114 0.47657 7.56972
59 3KO0 TFP 0.0459 0.40683 7.92079
60 1XI9 PLP 0.02098 0.41708 7.98479
61 2ZE3 AKG 0.03066 0.41447 7.98479
62 1M5W DXP 0.04762 0.40201 8.23045
63 5BVS EIC 0.0199 0.40702 8.33333
64 3WBG 2AN 0.02213 0.40147 8.49673
65 4EUO ABU 0.0121 0.43318 9.12547
66 2IMP LAC 0.01243 0.42978 9.88593
67 1O7Q GAL NAG 0.00003634 0.48526 10.6464
68 1O7Q UDP 0.00005686 0.46326 10.6464
69 4BXF AKG 0.03814 0.40791 10.6464
70 3GL0 HXX 0.02759 0.40343 10.6464
71 5KQA GSH 0.01844 0.42471 12.8788
72 1GA8 UPF 0.0000001608 0.58918 13.308
73 1GA8 DEL 0.0000001861 0.55465 13.308
74 4M5P 23W 0.02807 0.40702 14.4487
75 5N0F 7K2 0.02265 0.41868 17.1103
76 2Y69 CHD 0.02486 0.41954 22.5
Pocket No.: 2; Query (leader) PDB : 3U2U; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3u2u.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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