Receptor
PDB id Resolution Class Description Source Keywords
2PK3 1.82 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF A GDP-4-KETO-6-DEOXY-D-MANNOSE REDUCTAS ANEURINIBACILLUS THERMOAEROPHILUS SDR SHORT-CHAIN DEHYDROGENASE/REDUCTASE ROSSMANN FOLD OXIDOREDUCTASE
Ref.: THE STRUCTURAL BASIS FOR CATALYTIC FUNCTION OF GMD TWO CLOSELY RELATED ENZYMES FROM THE GDP-D-RHAMNOSE BIOSYNTHESIS PATHWAY. FEBS J. V. 276 2686 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A2R A:401;
B:402;
Valid;
Valid;
none;
none;
submit data
639.296 C15 H24 N5 O17 P3 c1nc(...
GDD A:410;
B:411;
Valid;
Valid;
none;
none;
submit data
605.341 C16 H25 N5 O16 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PK3 1.82 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF A GDP-4-KETO-6-DEOXY-D-MANNOSE REDUCTAS ANEURINIBACILLUS THERMOAEROPHILUS SDR SHORT-CHAIN DEHYDROGENASE/REDUCTASE ROSSMANN FOLD OXIDOREDUCTASE
Ref.: THE STRUCTURAL BASIS FOR CATALYTIC FUNCTION OF GMD TWO CLOSELY RELATED ENZYMES FROM THE GDP-D-RHAMNOSE BIOSYNTHESIS PATHWAY. FEBS J. V. 276 2686 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 352 families.
1 2PK3 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 2PK3 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 207 families.
1 1RPN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2PK3 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
3 1N7G - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 1T2A - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
5 5IN5 Kd = 35 uM GFB C16 H25 N5 O15 P2 C[C@H]1[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A2R; Similar ligands found: 318
No: Ligand ECFP6 Tc MDL keys Tc
1 A2R 1 1
2 ATR 0.825 0.957747
3 A22 0.821429 0.972222
4 NA7 0.784091 0.945946
5 A2P 0.772152 0.943662
6 AR6 0.72619 0.985915
7 APR 0.72619 0.985915
8 2AM 0.683544 0.930556
9 ENP 0.670213 0.932432
10 NPW 0.666667 0.875
11 25L 0.666667 0.972222
12 25A 0.655914 0.958333
13 NDP 0.650943 0.909091
14 XNP 0.648148 0.8625
15 TXP 0.64486 0.909091
16 NZQ 0.64486 0.897436
17 A2D 0.642857 0.958333
18 NJP 0.638889 0.933333
19 ODP 0.638889 0.897436
20 BA3 0.609195 0.958333
21 SAP 0.604396 0.933333
22 AGS 0.604396 0.933333
23 ADP 0.602273 0.985915
24 AP5 0.602273 0.958333
25 B4P 0.602273 0.958333
26 HEJ 0.6 0.985915
27 ATP 0.6 0.985915
28 HQG 0.6 1
29 AN2 0.595506 0.972222
30 AQP 0.593407 0.985915
31 5FA 0.593407 0.985915
32 M33 0.588889 0.945205
33 ADV 0.586957 0.945946
34 RBY 0.586957 0.945946
35 PAP 0.586957 0.971831
36 9X8 0.585859 0.933333
37 OAD 0.585859 0.958904
38 DG1 0.584746 0.909091
39 1DG 0.584746 0.909091
40 ADQ 0.581633 0.958904
41 OVE 0.581395 0.893333
42 AT4 0.577778 0.945946
43 2A5 0.576087 0.906667
44 V3L 0.574468 0.985915
45 3OD 0.574257 0.958904
46 TAP 0.571429 0.896104
47 AD9 0.569892 0.958904
48 7L1 0.566667 0.786517
49 ACP 0.565217 0.958904
50 NAP 0.563025 0.932432
51 ACQ 0.557895 0.958904
52 A3P 0.555556 0.957747
53 PO4 PO4 A A A A PO4 0.554455 0.890411
54 7D4 0.554348 0.893333
55 NA0 0.553719 0.92
56 APX 0.553398 0.921053
57 A 0.551724 0.957747
58 AMP 0.551724 0.957747
59 7D3 0.544444 0.893333
60 PRX 0.542553 0.881579
61 ANP 0.541667 0.958904
62 6YZ 0.540816 0.958904
63 3AM 0.54023 0.916667
64 ADX 0.537634 0.8625
65 CA0 0.537634 0.958904
66 PPS 0.536082 0.8625
67 A1R 0.534653 0.896104
68 A3R 0.534653 0.896104
69 KG4 0.531915 0.958904
70 50T 0.531915 0.945205
71 CO7 0.53125 0.795455
72 ATF 0.530612 0.945946
73 BIS 0.528846 0.921053
74 OMR 0.526786 0.864198
75 0WD 0.521368 0.909091
76 7D5 0.517241 0.866667
77 45A 0.516484 0.905405
78 ABM 0.516484 0.905405
79 SRA 0.511111 0.906667
80 APC 0.510417 0.945946
81 T99 0.510204 0.945946
82 TAT 0.510204 0.945946
83 AP2 0.505376 0.945946
84 A12 0.505376 0.945946
85 8LE 0.50505 0.907895
86 5AL 0.50505 0.945205
87 NAX 0.504425 0.8625
88 AV2 0.5 0.905405
89 00A 0.5 0.896104
90 NMN AMP PO4 0.495798 0.858974
91 AP0 0.495652 0.884615
92 AFH 0.495495 0.897436
93 5SV 0.495146 0.8375
94 8LH 0.49505 0.92
95 SRP 0.49505 0.92
96 3AT 0.494949 0.958333
97 ADP MG 0.494737 0.930556
98 NAI 0.491228 0.896104
99 DQV 0.491071 0.945205
100 4AD 0.490385 0.933333
101 AU1 0.489583 0.958904
102 FYA 0.485981 0.893333
103 DLL 0.485714 0.945205
104 8LQ 0.485437 0.92
105 48N 0.482456 0.909091
106 XYA 0.481928 0.833333
107 RAB 0.481928 0.833333
108 ADN 0.481928 0.833333
109 OZV 0.480769 0.958333
110 OOB 0.480769 0.945205
111 8QN 0.480769 0.945205
112 DTP 0.48 0.893333
113 6V0 0.478261 0.884615
114 TXD 0.478261 0.896104
115 PAJ 0.47619 0.897436
116 AMO 0.47619 0.945946
117 APC MG 0.474747 0.905405
118 ATP MG 0.474747 0.930556
119 ADP PO3 0.474747 0.930556
120 TXE 0.474138 0.896104
121 G3A 0.473214 0.909091
122 1ZZ 0.472222 0.851852
123 PTJ 0.472222 0.909091
124 AHX 0.471698 0.884615
125 MAP 0.471154 0.933333
126 UPA 0.470085 0.896104
127 DAT 0.469388 0.893333
128 G5P 0.469027 0.909091
129 AR6 AR6 0.469027 0.931507
130 LMS 0.467391 0.817073
131 3UK 0.46729 0.932432
132 ADP BMA 0.46729 0.932432
133 NXX 0.465517 0.945946
134 UP5 0.465517 0.907895
135 DND 0.465517 0.945946
136 GTA 0.464912 0.875
137 SON 0.463918 0.945946
138 9SN 0.463636 0.884615
139 LAD 0.462963 0.873418
140 WAQ 0.462963 0.896104
141 PR8 0.462963 0.8625
142 B5V 0.462963 0.92
143 N01 0.459677 0.893333
144 FA5 0.459459 0.92
145 ME8 0.458716 0.851852
146 TXA 0.458716 0.945946
147 NB8 0.458716 0.909091
148 139 0.458333 0.8625
149 ADJ 0.458333 0.864198
150 ALF ADP 0.456311 0.858974
151 ADP ALF 0.456311 0.858974
152 ETB 0.456 0.823529
153 DCA 0.456 0.813953
154 VO4 ADP 0.451923 0.918919
155 ADP VO4 0.451923 0.918919
156 80F 0.451613 0.853659
157 GAP 0.45098 0.906667
158 DDS 0.45098 0.866667
159 F2R 0.45082 0.876543
160 9BG 0.45082 0.884615
161 30N 0.449612 0.744681
162 0T1 0.448819 0.813953
163 COA 0.448819 0.813953
164 COD 0.447154 0.802326
165 B5M 0.446429 0.907895
166 B5Y 0.446429 0.907895
167 YAP 0.446429 0.907895
168 4TC 0.445378 0.884615
169 NDO 0.445312 0.906667
170 ITT 0.444444 0.930556
171 DAL AMP 0.443396 0.918919
172 CNA 0.442623 0.92
173 XAH 0.442478 0.829268
174 LQJ 0.442478 0.905405
175 A4P 0.441667 0.833333
176 APU 0.441667 0.883117
177 PUA 0.440945 0.873418
178 9ZD 0.439252 0.921053
179 9ZA 0.439252 0.921053
180 5AS 0.438776 0.770115
181 4UV 0.438596 0.907895
182 CAO 0.438462 0.786517
183 COS 0.438462 0.795455
184 AMX 0.438462 0.823529
185 TYM 0.436975 0.92
186 5N5 0.436782 0.808219
187 A A 0.436364 0.931507
188 LAQ 0.435897 0.851852
189 7D7 0.435294 0.733333
190 SCO 0.435115 0.835294
191 CMX 0.435115 0.835294
192 EAD 0.435115 0.8625
193 T5A 0.434426 0.831325
194 IVC 0.433824 0.804598
195 ATP A A A 0.433628 0.917808
196 ATP A 0.433628 0.917808
197 EP4 0.433333 0.74359
198 OXK 0.432836 0.816092
199 CA6 0.432836 0.721649
200 JB6 0.432432 0.871795
201 5CD 0.431818 0.794521
202 FCX 0.431818 0.806818
203 FAM 0.431818 0.795455
204 A4D 0.431818 0.808219
205 ACO 0.431818 0.786517
206 101 0.431579 0.866667
207 NVA 2AD 0.431373 0.75
208 GA7 0.431034 0.894737
209 4UU 0.431034 0.907895
210 GGZ 0.429907 0.814815
211 62F 0.429577 0.851852
212 HAX 0.428571 0.795455
213 128 0.428571 0.788235
214 4UW 0.428571 0.873418
215 A A A 0.427273 0.893333
216 G5A 0.427184 0.770115
217 JSQ 0.427184 0.933333
218 HFD 0.427184 0.933333
219 DA 0.427083 0.866667
220 D5M 0.427083 0.866667
221 AOC 0.427083 0.810811
222 3KK 0.425373 0.795455
223 FYN 0.425373 0.813953
224 12D 0.423729 0.797619
225 J4G 0.423423 0.933333
226 YZS 0.422222 0.721649
227 COK 0.422222 0.795455
228 KGP 0.422222 0.721649
229 SOP 0.422222 0.795455
230 P1H 0.422222 0.841463
231 MCD 0.422222 0.816092
232 G1R 0.420561 0.921053
233 YLP 0.420168 0.831325
234 CMC 0.419118 0.816092
235 CO6 0.419118 0.795455
236 1VU 0.419118 0.786517
237 NMX 0.419118 0.752688
238 6RE 0.416667 0.75
239 CAJ 0.416058 0.816092
240 SCD 0.416058 0.835294
241 FB0 0.416058 0.795455
242 2MC 0.416058 0.76087
243 MYR AMP 0.415929 0.829268
244 CA8 0.414286 0.721649
245 TYR AMP 0.413793 0.883117
246 MLC 0.413043 0.816092
247 M2T 0.413043 0.725
248 BCO 0.413043 0.795455
249 KGJ 0.413043 0.744681
250 A1S 0.413043 0.795455
251 3HC 0.413043 0.804598
252 DTA 0.413043 0.776316
253 1HE 0.413043 0.777778
254 AVV 0.412844 0.884615
255 NAD 0.412698 0.918919
256 BTX 0.412698 0.831325
257 1CZ 0.412587 0.806818
258 A3G 0.412371 0.789474
259 5X8 0.411765 0.776316
260 2VA 0.411765 0.789474
261 FAQ 0.411348 0.795455
262 CAA 0.410072 0.804598
263 LCV 0.410072 0.731959
264 SO5 0.410072 0.731959
265 YE1 0.410072 0.804598
266 MCA 0.410072 0.806818
267 COO 0.410072 0.795455
268 YLB 0.409836 0.831325
269 YLC 0.409836 0.851852
270 MTA 0.408602 0.763158
271 AYB 0.408 0.821429
272 SCA 0.407143 0.816092
273 YXS 0.407143 0.721649
274 2CP 0.407143 0.806818
275 MC4 0.407143 0.752688
276 YXR 0.407143 0.721649
277 ARG AMP 0.40678 0.841463
278 A U 0.406504 0.858974
279 A3D 0.40625 0.906667
280 6AD 0.40566 0.897436
281 NAE 0.40458 0.883117
282 3CP 0.404255 0.816092
283 BYC 0.404255 0.795455
284 1GZ 0.404255 0.786517
285 IRC 0.404255 0.804598
286 HGG 0.404255 0.816092
287 KGA 0.404255 0.755319
288 COW 0.404255 0.786517
289 COF 0.404255 0.777778
290 KFV 0.404255 0.729167
291 2KQ 0.404255 0.797753
292 TSB 0.40367 0.809524
293 TAD 0.403361 0.873418
294 IOT 0.403226 0.843373
295 S0N 0.402778 0.816092
296 CO8 0.402778 0.777778
297 HDV 0.401869 0.881579
298 R7I 0.401869 0.906667
299 A5A 0.401869 0.797619
300 R5I 0.401869 0.906667
301 V1N 0.401709 0.931507
302 AMP DBH 0.401709 0.906667
303 BCA 0.401408 0.786517
304 4CA 0.401408 0.786517
305 NHW 0.401361 0.777778
306 NHM 0.401361 0.777778
307 UOQ 0.401361 0.777778
308 ST9 0.4 0.777778
309 SO8 0.4 0.779221
310 3DH 0.4 0.763158
311 UCC 0.4 0.777778
312 AHZ 0.4 0.829268
313 YLA 0.4 0.831325
314 VRT 0.4 0.759494
315 DCC 0.4 0.777778
316 MFK 0.4 0.777778
317 MYA 0.4 0.777778
318 5F9 0.4 0.777778
Ligand no: 2; Ligand: GDD; Similar ligands found: 141
No: Ligand ECFP6 Tc MDL keys Tc
1 GDD 1 1
2 GDC 1 1
3 GKE 1 1
4 GFB 0.804124 0.974359
5 GDR 0.804124 0.974359
6 6CK 0.795918 0.95
7 GDX 0.772277 0.987013
8 GP3 0.755556 0.961538
9 GDP 0.747253 0.961039
10 JB2 0.745098 0.974359
11 GKD 0.745098 1
12 GSP 0.744681 0.91358
13 GTP 0.741935 0.961039
14 GNH 0.73913 0.948718
15 G1R 0.734043 0.974026
16 JB3 0.719626 0.962025
17 GPD 0.704762 0.938272
18 GCP 0.697917 0.936709
19 G 0.692308 0.948052
20 5GP 0.692308 0.948052
21 GNP 0.690722 0.936709
22 9GM 0.690722 0.936709
23 GPG 0.683168 0.974359
24 G2R 0.673267 0.925
25 GMV 0.670103 0.936709
26 G3A 0.660377 0.961538
27 G5P 0.654206 0.961538
28 GAV 0.643564 0.925
29 Y9Z 0.641509 0.892857
30 G2P 0.64 0.925
31 GP2 0.639175 0.925
32 GTG 0.635514 0.925926
33 GMP 0.625 0.87013
34 ADQ 0.61165 0.910256
35 U2G 0.608696 0.95
36 G4M 0.604651 0.916667
37 ALF 5GP 0.60396 0.857143
38 0O2 0.603774 0.948052
39 YGP 0.601852 0.891566
40 G4P 0.596154 0.948052
41 G3D 0.592233 0.948052
42 GDP AF3 0.584906 0.857143
43 GDP ALF 0.584906 0.857143
44 ALF GDP 0.584906 0.857143
45 CG2 0.584746 0.95
46 NGD 0.581197 0.949367
47 3GP 0.56701 0.935065
48 2MD 0.566667 0.882353
49 CAG 0.565574 0.872093
50 G G 0.5625 0.936709
51 FEG 0.554622 0.892857
52 MGD 0.552846 0.882353
53 ZGP 0.55 0.860465
54 GDP 7MG 0.53913 0.901235
55 TPG 0.539062 0.833333
56 KB7 0.538462 0.841463
57 MD1 0.535433 0.882353
58 PGD 0.535433 0.914634
59 2GP 0.535354 0.948052
60 FE9 0.527559 0.770833
61 DBG 0.527132 0.9375
62 A G 0.524194 0.924051
63 G A A A 0.524194 0.936709
64 U A G G 0.52 0.924051
65 G1R G1R 0.515385 0.9375
66 GH3 0.513761 0.935897
67 KBD 0.504425 0.864198
68 GCP G 0.5 0.886076
69 DGT 0.495413 0.888889
70 IDP 0.495238 0.935065
71 GPX 0.491071 0.910256
72 R5I 0.490741 0.935065
73 R7I 0.490741 0.935065
74 G U 0.488 0.91358
75 KBJ 0.487179 0.833333
76 DGI 0.485981 0.888889
77 G1G 0.484615 0.914634
78 BGO 0.48 0.9375
79 GPC 0.469231 0.892857
80 G C 0.46875 0.91358
81 PGD O 0.466667 0.842697
82 P2G 0.466667 0.897436
83 2GW 0.466102 0.792683
84 UPG 0.463636 0.8
85 GUD 0.463636 0.8
86 MGP 0.463636 0.925
87 GDU 0.463636 0.8
88 UFM 0.463636 0.8
89 C5G 0.460177 0.85
90 JBT 0.45977 0.810526
91 6G0 0.459459 0.925
92 P1G 0.457944 0.886076
93 GGM 0.457364 0.914634
94 AKW 0.456693 0.880952
95 HQG 0.455357 0.897436
96 DAU 0.448276 0.724138
97 IMP 0.447619 0.922078
98 GTA 0.447154 0.925926
99 DGP 0.443396 0.876543
100 DG 0.443396 0.876543
101 G U34 0.44186 0.902439
102 ADP BMA 0.435897 0.886076
103 APC G U 0.432836 0.876543
104 A2D 0.432692 0.884615
105 AGS 0.427273 0.841463
106 SAP 0.427273 0.841463
107 A G U 0.424658 0.902439
108 BA3 0.424528 0.884615
109 G G G RPC 0.424242 0.865854
110 G2Q 0.423729 0.925
111 ATP 0.422018 0.884615
112 HEJ 0.422018 0.884615
113 AP5 0.420561 0.884615
114 B4P 0.420561 0.884615
115 ADP 0.420561 0.884615
116 139 0.419847 0.845238
117 AR6 0.418182 0.884615
118 AQP 0.418182 0.884615
119 APR 0.418182 0.884615
120 5FA 0.418182 0.884615
121 AT4 0.416667 0.851852
122 AN2 0.416667 0.873418
123 G7M 0.416667 0.9125
124 G G G C 0.416058 0.902439
125 AD9 0.414414 0.8625
126 UCG 0.414286 0.901235
127 A22 0.413793 0.897436
128 A G C C 0.413043 0.901235
129 ITT 0.412844 0.835443
130 SGP 0.412844 0.819277
131 A G U U 0.410596 0.902439
132 ANP 0.40708 0.8625
133 ACQ 0.40708 0.8625
134 01G 0.406504 0.892857
135 1GW 0.40625 0.764706
136 DG DG 0.404959 0.879518
137 AFH 0.404762 0.855422
138 A4P 0.40458 0.882353
139 G C C C 0.401408 0.91358
140 M33 0.4 0.85
141 ATF 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PK3; Ligand: A2R; Similar sites found with APoc: 13
This union binding pocket(no: 1) in the query (biounit: 2pk3.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2GN4 NDP 14.0187
2 2GN4 UD1 14.0187
3 2GN4 NDP 14.0187
4 1EK6 UPG 42.9907
5 1EK6 NAI 42.9907
6 1EK6 UPG 42.9907
7 1EK6 NAI 42.9907
8 1KEW NAD 44.2368
9 1KEW TYD 44.2368
10 1ORR NAD 44.2368
11 1ORR NAD 44.2368
12 1KEW TYD 44.2368
13 1KEW NAD 44.2368
Pocket No.: 2; Query (leader) PDB : 2PK3; Ligand: A2R; Similar sites found with APoc: 14
This union binding pocket(no: 2) in the query (biounit: 2pk3.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2GN4 NDP 14.0187
2 2GN4 UD1 14.0187
3 2GN4 NDP 14.0187
4 1EK6 UPG 42.9907
5 1EK6 NAI 42.9907
6 1EK6 UPG 42.9907
7 1EK6 NAI 42.9907
8 1KEW NAD 44.2368
9 1KEW TYD 44.2368
10 1ORR NAD 44.2368
11 1ORR NAD 44.2368
12 1KEW TYD 44.2368
13 1KEW NAD 44.2368
14 4GLL NAD 44.5483
Pocket No.: 3; Query (leader) PDB : 2PK3; Ligand: GDD; 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: 2pk3.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2PK3; Ligand: GDD; 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: 2pk3.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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