Receptor
PDB id Resolution Class Description Source Keywords
1LRK 1.75 Å EC: 5.1.3.2 CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDP-GALACTOSE 4-EPIMER Y299C COMPLEXED WITH UDP-N-ACETYLGLUCOSAMINE ESCHERICHIA COLI EPIMERASE SHORT CHAIN DEHYDROGENASE GALACTOSEMIA ISOMERAS
Ref.: STRUCTURAL ANALYSIS OF THE Y299C MUTANT OF ESCHERIC UDP-GALACTOSE 4-EPIMERASE. TEACHING AN OLD DOG NEW J.BIOL.CHEM. V. 277 27528 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:342;
A:343;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
NAD A:340;
 Valid;
 none;
 submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
PGE A:344;
 Invalid;
 none;
 submit data
150.173 C6 H14 O4 C(COC...
UD1 A:341;
 Valid;
 none;
 submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1UDB 1.65 Å EC: 5.1.3.2 STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4- FLUORO-ALPHA-D-GLUCOSE ESCHERICHIA COLI UDP-GALACTOSE EPIMERASE ISOMERASE
Ref.: STRUCTURAL ANALYSIS OF UDP-SUGAR BINDING TO UDP-GAL 4-EPIMERASE FROM ESCHERICHIA COLI. BIOCHEMISTRY V. 36 6294 1997
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1XEL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1KVT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 1LRJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 1LRL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 1KVQ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1KVS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
7 2UDP - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1UDC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 1NAI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 1UDA Ki = 1.4 mM UFG C15 H23 F N2 O16 P2 C1=CN(C(=O....
11 1KVU - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
12 1A9Y - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
13 1LRK - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 1A9Z - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 1NAH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
16 1UDB Ki = 1.2 mM UFG C15 H23 F N2 O16 P2 C1=CN(C(=O....
17 1KVR - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1XEL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1KVT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 1LRJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 1LRL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 1KVQ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1KVS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
7 2UDP - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1UDC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 1NAI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 1UDA Ki = 1.4 mM UFG C15 H23 F N2 O16 P2 C1=CN(C(=O....
11 1KVU - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
12 1A9Y - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
13 1LRK - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 1A9Z - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 1NAH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
16 1UDB Ki = 1.2 mM UFG C15 H23 F N2 O16 P2 C1=CN(C(=O....
17 1KVR - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
18 1I3M - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
19 1I3K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
20 1EK5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
21 1HZJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
22 1EK6 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
23 1I3N - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 6K0I - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
25 6K0G - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1XEL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1KVT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 1LRJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 1LRL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 1KVQ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1KVS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
7 2UDP - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1UDC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 1NAI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 1UDA Ki = 1.4 mM UFG C15 H23 F N2 O16 P2 C1=CN(C(=O....
11 1KVU - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
12 1A9Y - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
13 1LRK - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 1A9Z - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 1NAH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
16 1UDB Ki = 1.2 mM UFG C15 H23 F N2 O16 P2 C1=CN(C(=O....
17 1KVR - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
18 1I3L - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
19 1I3M - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
20 1I3K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
21 1EK5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
22 1HZJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
23 1EK6 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
24 1I3N - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
25 6K0H - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
26 6K0I - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
27 6K0G - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
28 1GY8 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAD; Similar ligands found: 251
No: Ligand ECFP6 Tc MDL keys Tc
1 NAD IBO 0.885714 0.985915
2 NAD TDB 0.885714 0.985915
3 A3D 0.872727 0.986111
4 NHD 0.821429 0.972222
5 NAP 0.811966 0.986111
6 NFD 0.791304 0.946667
7 DND 0.765766 0.972603
8 AMP NAD 0.74359 0.972222
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 NDE 0.689922 0.972603
15 NAJ 0.683333 0.972222
16 NDC 0.679389 0.934211
17 NDO 0.674603 0.958904
18 N01 0.656 0.972222
19 CNA 0.642276 0.972603
20 NBP 0.621212 0.922078
21 NAD BBN 0.609929 0.876543
22 8ID 0.609756 0.922078
23 NAD CJ3 0.601399 0.845238
24 ADP MG 0.584906 0.957747
25 ADP BEF 0.584906 0.957747
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BA3 0.566038 0.958333
30 NAD NDT 0.565789 0.755319
31 M33 0.564815 0.918919
32 ADP PO3 0.563636 0.957747
33 ATP MG 0.563636 0.957747
34 AP5 0.560748 0.958333
35 B4P 0.560748 0.958333
36 BEF ADP 0.558559 0.931507
37 VO4 ADP 0.557522 0.932432
38 AT4 0.555556 0.894737
39 AN2 0.555556 0.918919
40 GAP 0.553571 0.932432
41 OOB 0.551724 0.972222
42 CA0 0.550459 0.932432
43 9JJ 0.546053 0.898734
44 ATP 0.545455 0.931507
45 HEJ 0.545455 0.931507
46 ACP 0.545455 0.906667
47 KG4 0.545455 0.932432
48 DQV 0.544 0.972222
49 ALF ADP 0.54386 0.883117
50 ANP MG 0.54386 0.945205
51 DAL AMP 0.543103 0.945205
52 8LQ 0.543103 0.92
53 AQP 0.540541 0.931507
54 APR 0.540541 0.931507
55 AR6 0.540541 0.931507
56 5FA 0.540541 0.931507
57 AGS 0.535714 0.883117
58 AD9 0.535714 0.906667
59 WAQ 0.533333 0.896104
60 ABM 0.53271 0.905405
61 45A 0.53271 0.905405
62 QA7 0.529915 0.907895
63 DLL 0.529412 0.972222
64 00A 0.529412 0.921053
65 AMP MG 0.528302 0.943662
66 ANP 0.526316 0.906667
67 NJP 0.526316 0.959459
68 ACQ 0.526316 0.906667
69 OAD 0.525 0.932432
70 ADX 0.522523 0.839506
71 8LE 0.521739 0.907895
72 5AL 0.521739 0.945205
73 A1R 0.521008 0.871795
74 9SN 0.520325 0.909091
75 A 0.518868 0.930556
76 AMP 0.518868 0.930556
77 50T 0.517857 0.893333
78 ATF 0.517241 0.894737
79 3OD 0.516393 0.932432
80 1ZZ 0.516393 0.851852
81 SON 0.513514 0.92
82 PRX 0.513274 0.881579
83 SRP 0.512821 0.92
84 8LH 0.512821 0.92
85 6YZ 0.512821 0.906667
86 3UK 0.512397 0.958904
87 9X8 0.512397 0.883117
88 ADP BMA 0.512397 0.932432
89 MYR AMP 0.512195 0.851852
90 NAJ PZO 0.510949 0.909091
91 NMN 0.509434 0.875
92 HQG 0.508475 0.918919
93 A3R 0.508333 0.871795
94 B5V 0.508197 0.945946
95 AMP DBH 0.507937 0.906667
96 A22 0.504202 0.945205
97 JNT 0.504132 0.906667
98 FA5 0.504 0.945946
99 ATP A 0.504 0.971831
100 ATP A A A 0.504 0.971831
101 B5M 0.504 0.933333
102 8QN 0.5 0.945205
103 NAX 0.496183 0.886076
104 PR8 0.495935 0.8625
105 ADQ 0.495868 0.932432
106 AMO 0.495868 0.92
107 4AD 0.495868 0.933333
108 PAJ 0.495868 0.873418
109 V2G 0.495726 0.884615
110 APC MG 0.495652 0.931507
111 A12 0.495495 0.894737
112 AP2 0.495495 0.894737
113 ALF ADP 3PG 0.492424 0.873418
114 AHZ 0.492308 0.851852
115 FYA 0.491935 0.918919
116 AHX 0.491803 0.884615
117 4UU 0.488372 0.933333
118 5SV 0.487603 0.8375
119 T99 0.487179 0.894737
120 TAT 0.487179 0.894737
121 APC 0.486957 0.894737
122 SRA 0.486239 0.881579
123 6V0 0.484848 0.909091
124 NAI 0.484848 0.921053
125 GTA 0.484615 0.898734
126 LAD 0.483871 0.873418
127 AU1 0.482456 0.906667
128 F2R 0.481752 0.831325
129 TXE 0.481203 0.921053
130 OMR 0.481203 0.841463
131 AF3 ADP 3PG 0.481203 0.873418
132 LAQ 0.480916 0.851852
133 G3A 0.48062 0.909091
134 B5Y 0.480315 0.933333
135 NB8 0.48 0.884615
136 TXA 0.48 0.92
137 BIS 0.48 0.871795
138 PTJ 0.48 0.884615
139 ME8 0.48 0.851852
140 139 0.477941 0.886076
141 LPA AMP 0.477273 0.851852
142 G5P 0.476923 0.909091
143 AFH 0.476923 0.873418
144 AR6 AR6 0.476923 0.958333
145 ARG AMP 0.476923 0.841463
146 25L 0.47619 0.945205
147 NAJ PYZ 0.475524 0.864198
148 9ZA 0.47541 0.896104
149 9ZD 0.47541 0.896104
150 OZV 0.47541 0.931507
151 25A 0.47541 0.958333
152 DZD 0.47482 0.897436
153 TXD 0.473684 0.921053
154 4UV 0.472868 0.933333
155 TYM 0.470149 0.945946
156 ADV 0.470085 0.894737
157 RBY 0.470085 0.894737
158 A7R 0.469231 0.857143
159 KMQ 0.46875 0.894737
160 4TA 0.467626 0.864198
161 48N 0.466165 0.884615
162 XAH 0.465116 0.851852
163 4UW 0.462687 0.897436
164 M24 0.461538 0.886076
165 80F 0.460993 0.853659
166 IOT 0.459854 0.821429
167 T5A 0.456522 0.853659
168 L3W 0.455882 0.92
169 EAD 0.455782 0.886076
170 MAP 0.455285 0.883117
171 GA7 0.454545 0.894737
172 BT5 0.453901 0.821429
173 A4P 0.452555 0.833333
174 UP5 0.451852 0.933333
175 PAP 0.445378 0.917808
176 AP0 0.445255 0.884615
177 4TC 0.445255 0.909091
178 YLP 0.444444 0.831325
179 P1H 0.443709 0.864198
180 AOC 0.442478 0.810811
181 Z5A 0.439189 0.833333
182 LMS 0.4375 0.817073
183 2A5 0.436975 0.857143
184 COD 0.43662 0.802326
185 ADJ 0.435714 0.841463
186 YLC 0.434783 0.851852
187 YLB 0.434783 0.831325
188 ATR 0.433333 0.90411
189 7MD 0.432836 0.851852
190 8X1 0.432 0.764045
191 G5A 0.429752 0.790698
192 PO4 PO4 A A A A PO4 0.429688 0.943662
193 TAD 0.42963 0.873418
194 D4F 0.428571 0.875
195 5AS 0.42735 0.770115
196 BTX 0.426573 0.831325
197 YLA 0.425532 0.831325
198 DSZ 0.425197 0.790698
199 NCN 0.424779 0.805556
200 UPA 0.42446 0.921053
201 8PZ 0.424242 0.811765
202 VMS 0.424 0.8
203 54H 0.424 0.8
204 9K8 0.423077 0.744444
205 N0B 0.422819 0.853659
206 6AD 0.422764 0.85
207 AYB 0.422535 0.821429
208 7D3 0.422414 0.844156
209 YLY 0.421769 0.821429
210 TSB 0.420635 0.809524
211 ODP 0.41958 0.922078
212 A5A 0.419355 0.819277
213 FB0 0.419355 0.775281
214 AV2 0.419355 0.855263
215 NNR 0.419048 0.739726
216 LEU LMS 0.418605 0.761364
217 649 0.417266 0.775281
218 H1Q 0.416667 0.917808
219 NMN AMP PO4 0.416667 0.933333
220 SSA 0.416 0.790698
221 P5A 0.415385 0.755556
222 LSS 0.414062 0.772727
223 52H 0.412698 0.790698
224 A2R 0.412698 0.918919
225 JB6 0.412214 0.896104
226 5N5 0.411215 0.783784
227 YSA 0.410448 0.811765
228 B1U 0.410448 0.786517
229 53H 0.409449 0.790698
230 5CA 0.409449 0.790698
231 ITT 0.408333 0.878378
232 7D4 0.408333 0.844156
233 NA7 0.407692 0.894737
234 5CD 0.407407 0.794521
235 0WD 0.406897 0.909091
236 A3P 0.40678 0.930556
237 HFD 0.406504 0.883117
238 JSQ 0.406504 0.883117
239 AVV 0.40625 0.860759
240 RAB 0.40566 0.808219
241 XYA 0.40566 0.808219
242 ADN 0.40566 0.808219
243 FDA 0.405063 0.823529
244 CUU 0.404959 0.905405
245 V47 0.404762 0.821918
246 GSU 0.40458 0.790698
247 7MC 0.404255 0.831325
248 NSS 0.403101 0.811765
249 6FA 0.402516 0.853659
250 PPS 0.4 0.817073
251 NVA LMS 0.4 0.784091
Ligand no: 2; 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
Similar Ligands (3D)
Ligand no: 1; Ligand: NAD; Similar ligands found: 4
No: Ligand Similarity coefficient
1 NAD 1.0000
2 NDP 0.9403
3 TXP 0.8813
4 NZQ 0.8708
Ligand no: 2; Ligand: UD1; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GDD 0.8671
2 TDX 0.8645
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1UDB; Ligand: UFG; Similar sites found with APoc: 6
This union binding pocket(no: 1) in the query (biounit: 1udb.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 1UAY ADN 11.157
2 1SB8 UD2 44.0828
3 6WJA NAD 49.3548
4 6WJA UD2 49.3548
5 6WJA UD2 49.3548
6 6WJA NAD 49.3548
Pocket No.: 2; Query (leader) PDB : 1UDB; Ligand: UFG; 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: 1udb.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1UDB; Ligand: NAD; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 1udb.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 1UAY ADN 11.157
2 1SB8 UD2 44.0828
3 6WJA NAD 49.3548
4 6WJA UD2 49.3548
5 6WJA UD2 49.3548
6 6WJA NAD 49.3548
Pocket No.: 4; Query (leader) PDB : 1UDB; Ligand: NAD; 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: 1udb.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
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