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Receptor
PDB id Resolution Class Description Source Keywords
2WOE 1.9 Å EC: 3.2.2.24 CRYSTAL STRUCTURE OF THE D97N VARIANT OF DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE (DRAG) FROM R HODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP-RIBOSE RHODOSPIRILLUM RUBRUM HYDROLASE DIMANGANESE NITROGEN FIXATION ADP-RIBOSYLGLYCOHYDROLASE MONO-ADP-RIBOSYLHYDROLASE
Ref.: MECHANISM OF ADP-RIBOSYLATION REMOVAL REVEALED BY T STRUCTURE AND LIGAND COMPLEXES OF THE DIMANGANESE MONO-ADP-RIBOSYLHYDROLASE DRAG. PROC.NATL.ACAD.SCI.USA V. 106 14247 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AR6 A:401;
B:401;
C:401;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
559.316 C15 H23 N5 O14 P2 c1nc(...
GOL A:600;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MN A:400;
B:400;
C:400;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
TLA A:500;
Invalid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WOE 1.9 Å EC: 3.2.2.24 CRYSTAL STRUCTURE OF THE D97N VARIANT OF DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE (DRAG) FROM R HODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP-RIBOSE RHODOSPIRILLUM RUBRUM HYDROLASE DIMANGANESE NITROGEN FIXATION ADP-RIBOSYLGLYCOHYDROLASE MONO-ADP-RIBOSYLHYDROLASE
Ref.: MECHANISM OF ADP-RIBOSYLATION REMOVAL REVEALED BY T STRUCTURE AND LIGAND COMPLEXES OF THE DIMANGANESE MONO-ADP-RIBOSYLHYDROLASE DRAG. PROC.NATL.ACAD.SCI.USA V. 106 14247 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2WOE - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2WOE - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2WOE - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AR6; Similar ligands found: 398
No: Ligand ECFP6 Tc MDL keys Tc
1 APR 1 1
2 AR6 1 1
3 A2D 0.898551 0.971831
4 BA3 0.847222 0.971831
5 B4P 0.835616 0.971831
6 AP5 0.835616 0.971831
7 M33 0.813333 0.958333
8 ADP 0.810811 0.971831
9 ADV 0.805195 0.958904
10 RBY 0.805195 0.958904
11 HEJ 0.802632 0.971831
12 ATP 0.802632 0.971831
13 AT4 0.8 0.932432
14 AN2 0.8 0.958333
15 5FA 0.792208 0.971831
16 AQP 0.792208 0.971831
17 AD9 0.782051 0.945205
18 AGS 0.782051 0.92
19 SAP 0.782051 0.92
20 ACP 0.779221 0.945205
21 A 0.753425 0.943662
22 AMP 0.753425 0.943662
23 3OD 0.747126 0.972222
24 PRX 0.746835 0.893333
25 9X8 0.744186 0.945946
26 OAD 0.744186 0.972222
27 CA0 0.74359 0.972222
28 ADX 0.74359 0.873418
29 ACQ 0.740741 0.945205
30 ANP 0.740741 0.945205
31 A22 0.738095 0.958333
32 50T 0.734177 0.931507
33 A2R 0.72619 0.985915
34 ABM 0.723684 0.917808
35 ATF 0.722892 0.932432
36 A1R 0.72093 0.907895
37 ADQ 0.72093 0.972222
38 A3R 0.72093 0.907895
39 6YZ 0.714286 0.945205
40 A12 0.705128 0.932432
41 AP2 0.705128 0.932432
42 SRA 0.697368 0.893333
43 5AL 0.690476 0.958333
44 APC 0.682927 0.932432
45 AU1 0.679012 0.945205
46 TAT 0.678571 0.932432
47 T99 0.678571 0.932432
48 SRP 0.674419 0.932432
49 BIS 0.67033 0.907895
50 25L 0.663043 0.958333
51 4AD 0.662921 0.945946
52 DLL 0.655556 0.958333
53 00A 0.655556 0.907895
54 ADP PO3 0.654762 0.943662
55 8QN 0.651685 0.958333
56 5SV 0.651685 0.848101
57 OOB 0.651685 0.958333
58 25A 0.651685 0.944444
59 DQV 0.649485 0.958333
60 PAJ 0.644444 0.909091
61 AMO 0.644444 0.958904
62 MAP 0.640449 0.92
63 OMR 0.64 0.875
64 AFH 0.639175 0.909091
65 AHX 0.637363 0.896104
66 FYA 0.634409 0.905405
67 3UK 0.630435 0.945205
68 NAX 0.63 0.873418
69 G3A 0.628866 0.896104
70 SON 0.626506 0.932432
71 ALF ADP 0.625 0.87013
72 ADP ALF 0.625 0.87013
73 B5V 0.623656 0.932432
74 PR8 0.623656 0.873418
75 WAQ 0.623656 0.907895
76 LAD 0.623656 0.884615
77 G5P 0.622449 0.896104
78 GAP 0.62069 0.918919
79 LMS 0.620253 0.82716
80 48N 0.62 0.921053
81 ADP VO4 0.617977 0.931507
82 VO4 ADP 0.617977 0.931507
83 AP0 0.617647 0.896104
84 ME8 0.617021 0.8625
85 TXA 0.617021 0.958904
86 PTJ 0.617021 0.896104
87 1ZZ 0.617021 0.8625
88 NB8 0.617021 0.921053
89 GTA 0.616162 0.8625
90 FA5 0.614583 0.932432
91 TXD 0.613861 0.907895
92 NAI 0.613861 0.907895
93 6V0 0.613861 0.896104
94 DND 0.613861 0.958904
95 NXX 0.613861 0.958904
96 TXE 0.607843 0.907895
97 DAL AMP 0.604396 0.931507
98 9SN 0.604167 0.896104
99 UP5 0.598039 0.92
100 YAP 0.597938 0.92
101 B5Y 0.597938 0.92
102 B5M 0.597938 0.92
103 9ZD 0.597826 0.907895
104 9ZA 0.597826 0.907895
105 XAH 0.591837 0.839506
106 RAB 0.589041 0.84507
107 ADN 0.589041 0.84507
108 XYA 0.589041 0.84507
109 2A5 0.586207 0.893333
110 4UV 0.585859 0.92
111 AOC 0.585366 0.821918
112 ADJ 0.584906 0.875
113 7D4 0.581395 0.88
114 ITT 0.581395 0.916667
115 A4P 0.580952 0.821429
116 ATR 0.579545 0.943662
117 PAP 0.579545 0.957747
118 CNA 0.579439 0.932432
119 ADP BMA 0.578947 0.945205
120 5AS 0.576471 0.77907
121 4UU 0.574257 0.92
122 GA7 0.574257 0.906667
123 F2R 0.574074 0.864198
124 5N5 0.573333 0.819444
125 7D3 0.571429 0.88
126 4TC 0.571429 0.896104
127 139 0.570093 0.873418
128 T5A 0.570093 0.841463
129 COD 0.568807 0.811765
130 JB6 0.56701 0.883117
131 A4D 0.565789 0.819444
132 5CD 0.565789 0.805556
133 EP4 0.564103 0.753247
134 LAQ 0.563107 0.8625
135 NA7 0.5625 0.932432
136 TYM 0.561905 0.932432
137 80F 0.558559 0.864198
138 YLP 0.557692 0.841463
139 A A 0.556701 0.917808
140 G5A 0.555556 0.77907
141 HFD 0.555556 0.92
142 4UW 0.552381 0.884615
143 ATP A A A 0.55 0.930556
144 AVV 0.547368 0.896104
145 A3P 0.546512 0.943662
146 MYR AMP 0.545455 0.839506
147 7D5 0.54321 0.853333
148 G1R 0.542553 0.907895
149 YLC 0.542056 0.8625
150 UPA 0.542056 0.907895
151 YLB 0.542056 0.841463
152 NAD 0.540541 0.931507
153 TYR AMP 0.539216 0.894737
154 AMP DBH 0.539216 0.918919
155 TAD 0.538462 0.884615
156 DTA 0.5375 0.786667
157 M2T 0.5375 0.734177
158 3DH 0.536585 0.773333
159 AYB 0.536364 0.831325
160 EAD 0.533898 0.873418
161 AHZ 0.533333 0.839506
162 FB0 0.532787 0.784091
163 IOT 0.53211 0.831325
164 A3D 0.530973 0.918919
165 MTA 0.530864 0.773333
166 3AM 0.53012 0.902778
167 ARG AMP 0.528846 0.829268
168 AR6 AR6 0.528846 0.944444
169 A2P 0.528736 0.929577
170 YLA 0.527273 0.841463
171 6AD 0.526882 0.884615
172 PPS 0.526882 0.85
173 BTX 0.526786 0.819277
174 NAE 0.525862 0.894737
175 BT5 0.522124 0.831325
176 A5A 0.521277 0.807229
177 TSB 0.520833 0.819277
178 6RE 0.517647 0.7375
179 P1H 0.516393 0.851852
180 3AT 0.516129 0.944444
181 SSA 0.515789 0.8
182 7MD 0.514286 0.886076
183 54H 0.510417 0.788235
184 52H 0.510417 0.77907
185 VMS 0.510417 0.788235
186 NSS 0.510204 0.8
187 NAQ 0.508475 0.871795
188 ZAS 0.505882 0.766234
189 IMO 0.505747 0.902778
190 J7C 0.505747 0.746835
191 A3N 0.505747 0.786667
192 AV2 0.505263 0.891892
193 R5I 0.505263 0.918919
194 R7I 0.505263 0.918919
195 53H 0.505155 0.77907
196 5CA 0.505155 0.8
197 8X1 0.505155 0.752809
198 ARU 0.50505 0.8375
199 NVA LMS 0.50505 0.752809
200 9K8 0.504951 0.733333
201 AF3 ADP 3PG 0.504587 0.860759
202 YLY 0.504274 0.831325
203 ZID 0.504202 0.918919
204 S4M 0.5 0.666667
205 V3L 0.5 0.971831
206 FDA 0.5 0.811765
207 LEU LMS 0.5 0.752809
208 DTP 0.5 0.88
209 LPA AMP 0.5 0.839506
210 2AM 0.5 0.916667
211 FNK 0.496183 0.784091
212 6FA 0.496063 0.841463
213 DZD 0.495652 0.884615
214 P5A 0.49505 0.744444
215 DSZ 0.494949 0.821429
216 LSS 0.494949 0.761364
217 MAO 0.494382 0.759036
218 DSH 0.494253 0.725
219 M24 0.491525 0.873418
220 NJP 0.491228 0.92
221 5X8 0.48913 0.786667
222 DAT 0.48913 0.88
223 SFD 0.488372 0.734043
224 FAS 0.488372 0.851852
225 FAD 0.488372 0.851852
226 NAJ PZO 0.487179 0.848101
227 0WD 0.486957 0.896104
228 NPW 0.486726 0.8625
229 7MC 0.486486 0.864198
230 7DT 0.483871 0.957747
231 7DD 0.483516 0.957747
232 GJV 0.483146 0.728395
233 OVE 0.482759 0.88
234 5AD 0.480519 0.746479
235 GSU 0.480392 0.8
236 KAA 0.480392 0.752809
237 NDE 0.48 0.906667
238 N0B 0.479339 0.841463
239 A5D 0.478723 0.786667
240 ODP 0.478261 0.884615
241 RGT 0.47619 0.958904
242 XNP 0.474138 0.85
243 4TA 0.474138 0.807229
244 AMP NAD 0.474138 0.931507
245 62F 0.473684 0.8625
246 NDP 0.473684 0.896104
247 SFG 0.473118 0.773333
248 NDC 0.472441 0.871795
249 YSA 0.471698 0.77907
250 NAJ PYZ 0.471074 0.807229
251 ENP 0.470588 0.918919
252 FAY 0.470149 0.8625
253 TXP 0.469565 0.896104
254 NZQ 0.469565 0.884615
255 DDS 0.46875 0.853333
256 A7D 0.467391 0.776316
257 RFL 0.466667 0.821429
258 ENQ 0.466019 0.943662
259 AAT 0.463918 0.707317
260 SA8 0.463158 0.728395
261 7C5 0.462963 0.818182
262 MHZ 0.462366 0.697674
263 8PZ 0.462264 0.8
264 71V 0.461538 0.883117
265 G A A A 0.461538 0.848101
266 F2N 0.460993 0.793103
267 NEC 0.460674 0.746667
268 A3G 0.460674 0.8
269 GGZ 0.46 0.825
270 6C6 0.458333 0.857143
271 SAH 0.458333 0.766234
272 SAI 0.458333 0.75641
273 P5F 0.457143 0.823529
274 Y3J 0.45679 0.726027
275 A A A 0.456311 0.905405
276 PO4 PO4 A A A A PO4 0.456311 0.902778
277 7D7 0.455696 0.743243
278 SMM 0.454545 0.705882
279 V1N 0.453704 0.944444
280 6IA 0.453608 0.814815
281 SAM 0.453608 0.710843
282 WSA 0.451327 0.788235
283 U A 0.45 0.883117
284 A G 0.449153 0.858974
285 EEM 0.44898 0.710843
286 PGS 0.446809 0.858974
287 ETB 0.446281 0.811765
288 DCA 0.446281 0.802326
289 U A G G 0.445378 0.858974
290 2SA 0.444444 0.932432
291 D5M 0.444444 0.853333
292 DA 0.444444 0.853333
293 GP3 0.443299 0.896104
294 9JJ 0.442857 0.8625
295 128 0.442478 0.776471
296 4YB 0.441441 0.781609
297 GEK 0.441176 0.759494
298 Z5A 0.44 0.77907
299 30N 0.44 0.734043
300 S7M 0.44 0.710843
301 AAM 0.43956 0.943662
302 0T1 0.439024 0.802326
303 COA 0.439024 0.802326
304 12D 0.4375 0.785714
305 FA9 0.4375 0.841463
306 C2R 0.436782 0.90411
307 AMZ 0.436782 0.890411
308 A3S 0.43617 0.810811
309 N6P 0.432692 0.888889
310 PUA 0.430894 0.860759
311 COS 0.428571 0.784091
312 TAP 0.428571 0.883117
313 AMX 0.428571 0.811765
314 1DG 0.428571 0.896104
315 CAO 0.428571 0.775281
316 AIR 0.428571 0.875
317 A6D 0.428571 0.722892
318 DG1 0.428571 0.896104
319 6K6 0.427184 0.90411
320 A3T 0.427083 0.821918
321 NIA 0.426966 0.8
322 649 0.426087 0.744444
323 GTP 0.425743 0.894737
324 SCO 0.425197 0.823529
325 CMX 0.425197 0.823529
326 G2R 0.424528 0.860759
327 GDP 0.424242 0.894737
328 7RA 0.423913 0.930556
329 OXK 0.423077 0.804598
330 0UM 0.423077 0.719512
331 8Q2 0.422414 0.772727
332 FCX 0.421875 0.795455
333 FAM 0.421875 0.784091
334 ACO 0.421875 0.775281
335 GCP 0.421569 0.871795
336 NAP 0.420635 0.918919
337 SXZ 0.420561 0.731707
338 GNH 0.42 0.883117
339 62X 0.419048 0.686047
340 A U 0.418803 0.87013
341 APU 0.418803 0.87013
342 HAX 0.418605 0.784091
343 NVA 2AD 0.418367 0.759494
344 GDC 0.418182 0.884615
345 GKE 0.418182 0.884615
346 GDD 0.418182 0.884615
347 101 0.417582 0.853333
348 GSP 0.417476 0.85
349 3AD 0.416667 0.805556
350 2MC 0.416667 0.75
351 HDV 0.415842 0.868421
352 FYN 0.415385 0.802326
353 3KK 0.415385 0.784091
354 G2Q 0.415094 0.860759
355 K15 0.415094 0.702381
356 NA0 0.414062 0.906667
357 7L1 0.414062 0.775281
358 IVC 0.413534 0.793103
359 S8M 0.413462 0.759494
360 NHD 0.413223 0.905405
361 7RP 0.413043 0.901408
362 MCD 0.412214 0.804598
363 SOP 0.412214 0.784091
364 CA6 0.412214 0.71134
365 COK 0.412214 0.784091
366 1VU 0.409091 0.775281
367 CO6 0.409091 0.784091
368 NMX 0.409091 0.741935
369 CMC 0.409091 0.804598
370 AS 0.408602 0.810127
371 QQY 0.406593 0.815789
372 ACK 0.406593 0.861111
373 6YU 0.40625 0.734043
374 CAJ 0.406015 0.804598
375 SCD 0.406015 0.823529
376 EO7 0.404255 0.788235
377 8BR 0.404255 0.881579
378 GNP 0.403846 0.871795
379 9GM 0.403846 0.871795
380 APX 0.40367 0.907895
381 KB1 0.40367 0.719512
382 TM1 0.40367 0.77381
383 SLU 0.403226 0.770115
384 BCO 0.402985 0.784091
385 MLC 0.402985 0.804598
386 3HC 0.402985 0.793103
387 1HE 0.402985 0.766667
388 A1S 0.402985 0.784091
389 1CZ 0.402878 0.795455
390 CC5 0.402439 0.816901
391 NMN AMP PO4 0.401639 0.87013
392 FAQ 0.40146 0.784091
393 COO 0.4 0.784091
394 YE1 0.4 0.793103
395 MCA 0.4 0.795455
396 CAA 0.4 0.793103
397 2BA 0.4 0.915493
398 CMP 0.4 0.901408
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WOE; Ligand: AR6; Similar sites found with APoc: 78
This union binding pocket(no: 1) in the query (biounit: 2woe.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3BF1 PAU 1.60643
3 4ETZ C2E 1.6835
4 4DDY DN6 1.90114
5 4YMZ 13P 1.99203
6 2F5X ASP 2.00669
7 3NY4 SMX 2.26415
8 2OG2 MLI 2.34114
9 3B9Q MLI 2.34114
10 5SXS NIZ 2.34114
11 2AWN ADP 2.34114
12 3WGT FAD 2.34114
13 5NM7 GLY 2.63158
14 6ACS CIT 2.71318
15 5MUA GAL 2.7972
16 3ITJ CIT 3.01003
17 4TQK NAG 3.01003
18 4IEE AGS 3.01003
19 4UP4 GAL NAG 3.01003
20 2GNK ATP 3.57143
21 5BWD FUM 3.67893
22 2H3H BGC 3.67893
23 1U72 MTX 3.76344
24 1U72 NDP 3.76344
25 3KIF GDL 3.77358
26 1KR3 113 3.87931
27 5LQ8 GB 3.90071
28 1FQK ALF 4.01338
29 3X01 AMP 4.07125
30 3RG9 NDP 4.16667
31 3RG9 WRA 4.16667
32 3KJS NAP 4.34783
33 3LGS ADE 4.49438
34 6F5W KG1 4.68227
35 5BSH PRO 4.69314
36 2PZE ATP 4.80349
37 1G4U AF3 4.8913
38 2NGR AF3 5.2356
39 5E5U MLT 5.30303
40 5E5U MLI 5.30303
41 5TCI MLI 5.35117
42 4MOP 2H5 5.35117
43 3IA4 NDP 5.55556
44 3AXB PRO 6.02007
45 3AXB FAD 6.02007
46 3KC1 2T6 6.02007
47 3S5W NAP 6.02007
48 1WQ1 AF3 6.62651
49 4OR7 NAP 6.66667
50 5JBX MLI 6.89655
51 2RGO FAD 7.02341
52 4JLS 3ZE 7.23684
53 5KBE IPH 7.42358
54 2J5V PCA 7.69231
55 1Q19 SSC 7.69231
56 5C9P FUC 8.02676
57 3K5I AIR 8.02676
58 4ZRN NAD 8.02676
59 5Z20 OXM 8.11594
60 5A96 GTP 8.43373
61 1HE1 AF3 8.88889
62 5URY PAM 8.90411
63 4U00 ADP 9.83607
64 6HKE MLT 10.3774
65 6HKE LMR 10.3774
66 4GQP B40 10.4418
67 4K7O EKZ 10.7023
68 1LTT GAL BGC 11.6505
69 1LT3 GAL BGC 11.6505
70 4F8L AES 11.7241
71 2D2F ADP 12.4
72 5WL1 CUY 15.1515
73 5WL1 D3D 15.1515
74 3QDV NDG 17.4825
75 4PYA 2X3 19.2547
76 5ZQY AR6 34.7826
77 6G28 AR6 40.8027
78 6G1P CIT 43.4783
Pocket No.: 2; Query (leader) PDB : 2WOE; Ligand: AR6; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 2woe.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1UNQ 4IP None
2 4CQK PIO None
3 1ND4 KAN 1.51515
4 5MB4 NAG 1.67224
5 1I0B PEL 1.67224
6 5C79 PBU 2
7 5TSH ANP 2.00669
8 4FWE FAD 2.00669
9 2OG7 AHB 2.00669
10 1T3D CYS 2.07612
11 1AOE GW3 2.08333
12 1AOE NDP 2.08333
13 5XSS XYP 2.34114
14 2PL3 ADP 2.54237
15 3NB0 G6P 2.67559
16 1P4V GLY 2.71186
17 2AF6 BRU 2.71318
18 5Z21 OXM 3.01003
19 5BJX NAD 3.34448
20 3RK0 AMP 4.34783
21 5L2R MLA 5.01672
22 5I34 GDP 5.01672
23 1GRN AF3 5.2356
24 3EYY MLI 6.2069
25 2DBX GLU 6.31579
26 4L8F MTX 7.02341
27 5HSA FAS 8.02676
28 3EEL 53T 11.4537
29 1TL2 NDG 11.8644
30 5KK4 44E 12.5
31 4WBD CIT 19.0635
32 4OGQ 7PH 20.5882
Pocket No.: 3; Query (leader) PDB : 2WOE; Ligand: AR6; Similar sites found with APoc: 24
This union binding pocket(no: 3) in the query (biounit: 2woe.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4USI AKG 1.2987
2 4I9B 1KA 1.33779
3 4RM0 FUC NAG GAL 1.67224
4 4RM0 FUC NDG GAL 1.67224
5 3B8I OXL 1.74216
6 4BVA NDP 2.00669
7 4BHL ARG 2.34114
8 5GQI CTP 2.42915
9 5D6T NGA 2.57353
10 4RJK PYR 2.67559
11 2F9W PAU 2.95203
12 1NAA 6FA 3.01003
13 1V59 FAD 3.34448
14 2BL9 CP6 3.36134
15 2BL9 NDP 3.36134
16 1T5C ADP 4.01338
17 2RGJ FAD 4.34783
18 2DRC MTX 6.91824
19 5EYW PGA 8.03213
20 1GQY ACP 9.0301
21 16PK BIS 9.36455
22 5U83 ZN8 13.6792
23 4ZGM 32M 16.129
24 2NV2 GLN 17.6471
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