Receptor
PDB id Resolution Class Description Source Keywords
4EDF 2.08 Å EC: 1.1.1.22 DIMERIC HUGDH, K94E HOMO SAPIENS OLIGOMERIC STATE MOLECULAR SWITCH MEDIUM CHAIN DEHYDROGENAGLUCURONIDATION MDR ROSSMANN FOLD OXIDOREDUCTASE
Ref.: COFACTOR BINDING TRIGGERS A MOLECULAR SWITCH TO ALLOSTERICALLY ACTIVATE HUMAN UDP-{ALPHA}-D-GLUCOSE 6-DEHYDROGENASE. BIOCHEMISTRY V. 51 9364 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UPG A:501;
B:501;
C:501;
D:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 33 uM
566.302 C15 H24 N2 O17 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4EDF 2.08 Å EC: 1.1.1.22 DIMERIC HUGDH, K94E HOMO SAPIENS OLIGOMERIC STATE MOLECULAR SWITCH MEDIUM CHAIN DEHYDROGENAGLUCURONIDATION MDR ROSSMANN FOLD OXIDOREDUCTASE
Ref.: COFACTOR BINDING TRIGGERS A MOLECULAR SWITCH TO ALLOSTERICALLY ACTIVATE HUMAN UDP-{ALPHA}-D-GLUCOSE 6-DEHYDROGENASE. BIOCHEMISTRY V. 51 9364 2012
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2Q3E - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 5TJH - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 2QG4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3KHU - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
5 4EDF Kd = 33 uM UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
6 3PTZ - UDX C14 H22 N2 O16 P2 C1[C@H]([C....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2Q3E - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 5TJH - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 2QG4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3KHU - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
5 4EDF Kd = 33 uM UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
6 3PTZ - UDX C14 H22 N2 O16 P2 C1[C@H]([C....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2Q3E - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 5TJH - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 2QG4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3KHU - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
5 4EDF Kd = 33 uM UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
6 3PTZ - UDX C14 H22 N2 O16 P2 C1[C@H]([C....
7 2Y0E - UGA C15 H22 N2 O18 P2 C1=CN(C(=O....
8 2Y0C - UGA C15 H22 N2 O18 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UPG; Similar ligands found: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 GDU 1 1
2 UFM 1 1
3 UPG 1 1
4 GUD 1 1
5 USQ 0.8 0.846154
6 UFG 0.797619 0.943662
7 U2F 0.797619 0.943662
8 UPF 0.797619 0.943662
9 UD1 0.73913 0.985294
10 UD2 0.73913 0.985294
11 UGB 0.738636 0.985075
12 UGA 0.738636 0.985075
13 UDP 0.717949 0.941176
14 UDX 0.715909 0.970588
15 UAD 0.715909 0.970588
16 UDP GAL 0.715909 0.970588
17 UTP 0.7125 0.941176
18 IUG 0.693878 0.835443
19 G3N 0.692308 0.942857
20 C5G 0.688889 0.943662
21 URM 0.681818 0.956522
22 660 0.681818 0.956522
23 UPU 0.670588 0.970149
24 EPZ 0.650485 0.971014
25 3UC 0.648936 0.943662
26 UNP 0.647059 0.914286
27 EEB 0.644231 0.957143
28 EPU 0.644231 0.957143
29 U5P 0.641026 0.926471
30 HP7 0.636364 0.970588
31 UD7 0.636364 0.956522
32 2GW 0.632653 0.957143
33 MJZ 0.63 0.942857
34 UD4 0.623762 0.942857
35 UDH 0.615385 0.866667
36 UPP 0.615385 0.942029
37 UDZ 0.615385 0.88
38 UMA 0.598214 0.971014
39 44P 0.597561 0.901408
40 UDM 0.59596 0.942857
41 12V 0.592233 0.929577
42 HWU 0.592233 0.929577
43 1GW 0.590476 0.917808
44 2KH 0.586207 0.914286
45 Y6W 0.585106 0.916667
46 UDP UDP 0.576471 0.911765
47 U22 0.567797 0.8375
48 U21 0.567797 0.858974
49 U20 0.567797 0.858974
50 URI 0.552632 0.865672
51 U 0.552632 0.865672
52 CJB 0.551282 0.850746
53 UP5 0.527273 0.855263
54 UAG 0.523438 0.917808
55 2QR 0.520325 0.848101
56 DAU 0.519608 0.891892
57 U3P 0.511905 0.911765
58 UA3 0.511905 0.911765
59 CSQ 0.504762 0.878378
60 CSV 0.504762 0.878378
61 4TC 0.504425 0.833333
62 U U 0.5 0.927536
63 4RA 0.492308 0.857143
64 UD0 0.484848 0.846154
65 PUP 0.480392 0.887324
66 UML 0.478571 0.858974
67 U2P 0.476744 0.926471
68 CXY 0.471154 0.916667
69 GDD 0.463636 0.8
70 GKE 0.463636 0.8
71 GDC 0.463636 0.8
72 A U 0.461538 0.831169
73 CTP 0.447917 0.888889
74 CDP 0.446809 0.888889
75 CH 0.444444 0.861111
76 ADQ 0.443396 0.828947
77 DKX 0.44186 0.774648
78 U2S 0.43956 0.77027
79 UMF 0.438202 0.833333
80 U4S 0.433333 0.733333
81 DUT 0.43299 0.861111
82 U3S 0.423913 0.756757
83 5GW 0.421569 0.915493
84 DUD 0.421053 0.861111
85 5FU 0.417582 0.863014
86 C2G 0.417476 0.902778
87 UPA 0.416667 0.868421
88 7XL 0.415842 0.890411
89 U1S 0.415842 0.776316
90 U U U U 0.413462 0.913043
91 2TU 0.411765 0.777778
92 UTP U U U 0.409524 0.897059
93 139 0.406504 0.835443
94 APU 0.401639 0.831169
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EDF; Ligand: UPG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4edf.bio2) has 103 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4EDF; Ligand: UPG; Similar sites found: 203
This union binding pocket(no: 2) in the query (biounit: 4edf.bio2) has 104 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MQ6 NDP 0.007547 0.41953 1.417
2 1M2W NAD 0.0004638 0.47326 1.41988
3 4D3F NAP 0.0000368 0.5267 1.6129
4 1GQ2 NAP 0.002378 0.42726 1.61943
5 2BH9 NAP 0.01429 0.42492 1.63599
6 2YVF NAD 0.001138 0.40989 1.71569
7 2YVF FAD 0.00108 0.40989 1.71569
8 5EOW FAD 0.003614 0.40809 1.7284
9 4UP4 NAG 0.04545 0.41464 1.74564
10 4UP4 NDG 0.04545 0.41464 1.74564
11 2X3N FAD 0.00322 0.40364 1.75439
12 4GKV NAD 0.001232 0.42577 1.78571
13 4E5N NAD 0.0007141 0.44278 1.81818
14 1PGP 6PG 0.000172 0.40103 1.86722
15 5CAE COA 0.001641 0.44569 1.91693
16 5CAE SIN 0.004768 0.40567 1.91693
17 5FI3 NAP 0.002739 0.42218 1.96078
18 3AXB FAD 0.002665 0.40662 2.00893
19 2QA1 FAD 0.001383 0.42149 2.02429
20 2FZW NAD 0.0003878 0.40631 2.14477
21 2F1K NAP 0.00001683 0.52333 2.15054
22 5VN0 NAI 0.0003012 0.47057 2.22672
23 5D4V SAH 0.003227 0.43906 2.23881
24 1EQ2 NAP 0.008312 0.40278 2.25806
25 5H81 NAP 0.00005696 0.51815 2.31362
26 1ZMD NAI 0.0002192 0.48001 2.32068
27 2IZ1 ATR 0.0005426 0.44466 2.32068
28 2PV7 NAD 0.00008116 0.49075 2.34899
29 4MDH NAD 0.01125 0.40193 2.39521
30 1V6A TRE 0.0005879 0.52457 2.40964
31 1D1T NAD 0.0001492 0.46649 2.41287
32 4K5S FAD 0.001212 0.42851 2.42915
33 3FWN ATR 0.00008382 0.40699 2.5
34 1V8B NAD 0.0001042 0.4062 2.50522
35 1P77 ATR 0.00106 0.50752 2.57353
36 4TXI FAD 0.001375 0.42893 2.63158
37 3V1Y NAD 0.0001263 0.48647 2.67062
38 1U3U NAD 0.001142 0.40933 2.6738
39 2HJR APR 0.00005343 0.51485 2.7439
40 4FN4 NAD 0.007112 0.40551 2.75591
41 1J5P NAD 0.0006795 0.45252 2.7668
42 3M6W SAM 0.04174 0.40152 2.80172
43 2VPN 4CS 0.04929 0.41603 2.8481
44 3TWO NDP 0.002855 0.40976 2.87356
45 3WBF NAP 0.001329 0.43757 2.95082
46 3WBF API 0.001276 0.42766 2.95082
47 5T9F TYR 0.0005232 0.43223 2.95203
48 5T9F NAP 0.0007693 0.42855 2.95203
49 1YQD NAP 0.002824 0.41441 3.03644
50 3OND NAD 0.0006153 0.40839 3.07377
51 3OND ADN 0.0006153 0.40839 3.07377
52 5KVS NAP 0.003339 0.43224 3.11688
53 5KVS 6XR 0.005278 0.40398 3.11688
54 5EVY FAD 0.01481 0.40649 3.23887
55 1WDK NAD 0.000006102 0.4 3.23887
56 1Z82 NDP 0.0002032 0.47424 3.28358
57 2DT5 NAD 0.00005996 0.49245 3.31754
58 2GCG NDP 0.003536 0.42022 3.33333
59 4DPL NAP 0.003526 0.41777 3.34262
60 3Q3C NAD 0.00001762 0.4 3.34448
61 4K28 NAD 0.0002235 0.47965 3.34572
62 1QMG APX 0.01723 0.40355 3.4413
63 3B1F NAD 0.0000685 0.51454 3.44828
64 4CJX NAP 0.002218 0.43696 3.44828
65 4OOE NDP 0.006501 0.41433 3.46535
66 3H9E NAD 0.0004776 0.46213 3.46821
67 4RDH AMP 0.02004 0.41757 3.47222
68 2GSD NAD 0.002733 0.41047 3.48259
69 1LLU NAD 0.00127 0.42527 3.50877
70 4XDY NAI 0.001952 0.43637 3.5503
71 2B6N ALA PRO THR 0.01862 0.43306 3.59712
72 4D79 ATP 0.00563 0.43782 3.62319
73 2RAB NAD 0.001785 0.40625 3.67171
74 1C3V NDP 0.0005242 0.44809 3.67347
75 4J4H NAI 0.0006497 0.40575 3.861
76 4J4H 1J1 0.0006497 0.40575 3.861
77 2YGM GLA NAG GAL FUC 0.04 0.41566 3.9548
78 3GFB NAD 0.0004902 0.45839 4
79 3HAD NAD 0.0000614 0.43686 4.04858
80 4JBI NDP 0.003246 0.42986 4.05405
81 1NVM NAD 0.0007278 0.44245 4.05797
82 1NYT NAP 0.005775 0.41913 4.05904
83 3WV8 ATP 0.0004151 0.48747 4.12844
84 5VKT NAP 0.002624 0.42293 4.14365
85 1VQW FAD 0.005038 0.40475 4.15755
86 1SQF SAM 0.009839 0.42622 4.1958
87 1UXG NAD 0.0001284 0.40963 4.20712
88 1BW9 NAD 0.0002918 0.48616 4.21348
89 1HDG NAD 0.004475 0.42388 4.21687
90 1C1X NAD 0.0005499 0.45955 4.22535
91 1PZG A3D 0.0006737 0.42825 4.22961
92 2GV8 NDP 0.006653 0.41917 4.25056
93 2GV8 FAD 0.004115 0.40595 4.25056
94 2CVQ NDP 0.004668 0.41529 4.28135
95 5E4R NAP 0.00671 0.40885 4.28571
96 2NXE SAM 0.02237 0.40909 4.33071
97 3NJ4 NAD 0.001908 0.42634 4.36782
98 3NJ4 AFX 0.002227 0.42391 4.36782
99 5U5G NAP 0.00006259 0.49169 4.40678
100 5U5G 7VD 0.005898 0.46609 4.40678
101 5LD5 NAD 0.003425 0.43477 4.46927
102 2RGJ FAD 0.002934 0.41377 4.47761
103 9LDB NAD 0.00005906 0.48557 4.51807
104 1E3I CXF 0.0003572 0.44078 4.52128
105 5LKC FUC GLA A2G 0.039 0.41131 4.54545
106 5M67 NAD 0.0004223 0.41455 4.5929
107 5M67 ADE 0.0004269 0.4144 4.5929
108 5M67 3D1 0.0004898 0.4125 4.5929
109 5TUF FAD 0.001651 0.42583 4.64548
110 2ZJ1 NAD 0.0004167 0.40553 4.65587
111 1Y1P NMN AMP PO4 0.008906 0.41633 4.67836
112 2B5W NAP 0.004536 0.40226 4.7619
113 5CX8 3DO 0.03228 0.41942 4.7817
114 1I0Z NAI 0.0001054 0.47898 4.8048
115 1VI2 NAD 0.001319 0.4566 5
116 3OA2 NAD 0.002337 0.42756 5.03145
117 4O0L NDP 0.006625 0.40449 5.09091
118 2GLX NDP 0.00428 0.42754 5.12048
119 2Q0L NAP 0.001096 0.48038 5.14469
120 1NPD NAD 0.001184 0.45187 5.20833
121 3JV7 NAD 0.0003207 0.45959 5.21739
122 1O0S NAI 0.0005715 0.46925 5.26316
123 3WMX NAD 0.004182 0.42242 5.30726
124 5UC9 MYR 0.04722 0.40174 5.30973
125 1A5Z NAD 0.0001235 0.503 5.32915
126 1ZEM NAD 0.00521 0.41839 5.34351
127 2YVJ NAI 0.0001715 0.51016 5.50459
128 3OFK SAH 0.03338 0.40348 5.55556
129 1P31 EPU 0.0194 0.41207 5.68421
130 3BAZ NAP 0.001523 0.44396 5.70571
131 3KLJ FAD 0.005799 0.4024 5.71429
132 2AHR NAP 0.007752 0.40178 5.79151
133 3VPH OXM 0.0001308 0.45966 5.80645
134 3VPH NAD 0.000312 0.45113 5.80645
135 3JUC PCA 0.04326 0.41107 5.88235
136 2NU8 COA 0.001357 0.44303 5.90278
137 3GGO ENO 0.0001273 0.41744 6.05096
138 3GGO NAI 0.0001273 0.41744 6.05096
139 4XDZ NDP 0.005601 0.4197 6.12245
140 1YKF NAP 0.0006553 0.44713 6.25
141 1KEV NDP 0.0001597 0.45932 6.26781
142 3ABI NAD 0.0004388 0.45412 6.30137
143 2VOH CIT 0.01649 0.43239 6.36943
144 4YCA NDP 0.000008836 0.5351 6.46258
145 1TB4 PEJ 0.003159 0.41968 6.469
146 1YRX FMN 0.04969 0.40059 6.61157
147 5I39 FAD 0.00313 0.40207 6.61765
148 1U1I NAD 0.005678 0.40065 6.63265
149 4XYB NDP 0.00147 0.42287 6.64962
150 1LDM NAD 0.00008414 0.48292 6.68693
151 3EWP APR 0.01365 0.40552 6.77966
152 1HYH NAD 0.0002205 0.46295 6.79612
153 5JE8 NAD 0.000005199 0.54958 6.95364
154 1HKU NAD 0.0003178 0.45668 6.98324
155 1VPD TLA 0.01115 0.44699 7.02341
156 4URG C2E 0.02368 0.43073 7.18563
157 1ZQ9 SAM 0.01899 0.41252 7.36842
158 4JJF N2I 0.002438 0.42421 7.55814
159 4JJF FE9 0.004156 0.4199 7.55814
160 2I3G NAP 0.003578 0.41509 7.67045
161 5UAV TFB 0.0000446 0.41708 7.76398
162 5UAV NDP 0.0000446 0.41708 7.76398
163 1H2B NAJ 0.0004482 0.44509 7.79944
164 1YJQ NAP 0.00006278 0.40618 7.92079
165 1WP4 NDP 0.000005303 0.53984 7.95848
166 2IXB NAD 0.004176 0.41243 8.10811
167 3CGD COA 0.002906 0.40533 8.54167
168 3CGD FAD 0.002906 0.40533 8.54167
169 3CGD NAD 0.002906 0.40533 8.54167
170 5KKA 6V0 0.001578 0.4266 8.65385
171 1CER NAD 0.0009697 0.44918 8.76133
172 4XZ3 COA 0.0006761 0.46601 8.83621
173 3LZW FAD 0.00131 0.41559 9.03614
174 1DIG NAP 0.006762 0.40195 9.15033
175 4KOA NDP 0.004165 0.44774 9.30931
176 1JAY NAP 0.0018 0.45051 9.43396
177 5EZ7 FAD 0.002834 0.40163 9.43878
178 3QH2 3NM 0.03762 0.42103 9.95475
179 2VHW NAI 0.0001525 0.4045 10.0796
180 1EZ4 NAD 0.0001674 0.48131 10.3774
181 1OBB NAD 0.004709 0.42573 10.4167
182 5DN9 NAD 0.001089 0.4303 10.7143
183 5AYV KPL 0.00003347 0.4193 11.0032
184 5GZ6 NDP 0.0006459 0.47445 11.0429
185 5GZ6 7C3 0.0005049 0.47163 11.0429
186 1F8F NAD 0.0004209 0.46787 12.1294
187 2EV9 SKM 0.002693 0.41755 12.1673
188 1O94 ADP 0.0003082 0.47733 12.1875
189 4RQU NAD 0.0001774 0.47325 12.2667
190 5ODQ FAD 0.001787 0.40275 12.8571
191 5L95 AMP 0.0137 0.41631 13.75
192 2CVZ NDP 0.000006587 0.54048 14.5329
193 3QV1 NAD 0.001801 0.44083 18.2927
194 1LVL NAD 0.0002184 0.49608 18.7773
195 4R5M NAP 0.003488 0.42047 19.4149
196 4R5M 4NO 0.006095 0.40593 19.4149
197 1LTH NAD 0.00002327 0.52619 26.9592
198 3B1J NAD 0.001774 0.42976 28
199 1MUU GDX 0.000000002824 0.70432 38.7615
200 1MUU NAD 0.00000003234 0.64402 38.7615
201 1MV8 GDX 0.000000003165 0.47895 39.2202
202 1MV8 NAD 0.00000003391 0.46707 39.2202
203 3OJO NAD 0.000002453 0.40859 43.8515
Pocket No.: 3; Query (leader) PDB : 4EDF; Ligand: UPG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4edf.bio1) has 103 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4EDF; Ligand: UPG; Similar sites found: 4
This union binding pocket(no: 4) in the query (biounit: 4edf.bio1) has 104 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1H0A I3P 0.03951 0.41649 2.53165
2 5GUD NDP 0.002611 0.40107 7.64331
3 5N53 8NB 0.03491 0.42256 9.74359
4 2FKA BEF 0.0428 0.41853 12.4031
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