Receptor
PDB id Resolution Class Description Source Keywords
1MK1 2 Å EC: 3.6.1.13 STRUCTURE OF THE MT-ADPRASE IN COMPLEX WITH ADPR, A NUDIX EN MYCOBACTERIUM TUBERCULOSIS NUDIX HYDROLASE ADPR PYROPHOSPHATASE ADPRASE ADENOSINE DIRIBOSE MYCOBACTERIUM TUBERCULOSIS RV1700 HYDROLASE
Ref.: STRUCTURE AND MECHANISM OF MT-ADPRASE, A NUDIX HYDR FROM MYCOBACTERIUM TUBERCULOSIS STRUCTURE V. 11 1015 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
APR A:208;
Valid;
none;
submit data
559.316 C15 H23 N5 O14 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MK1 2 Å EC: 3.6.1.13 STRUCTURE OF THE MT-ADPRASE IN COMPLEX WITH ADPR, A NUDIX EN MYCOBACTERIUM TUBERCULOSIS NUDIX HYDROLASE ADPR PYROPHOSPHATASE ADPRASE ADENOSINE DIRIBOSE MYCOBACTERIUM TUBERCULOSIS RV1700 HYDROLASE
Ref.: STRUCTURE AND MECHANISM OF MT-ADPRASE, A NUDIX HYDR FROM MYCOBACTERIUM TUBERCULOSIS STRUCTURE V. 11 1015 2003
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1MR2 - A12 C11 H17 N5 O9 P2 c1nc(c2c(n....
2 1MK1 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
3 1MQE - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
4 1MQW - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1MR2 - A12 C11 H17 N5 O9 P2 c1nc(c2c(n....
2 1MK1 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
3 1MQE - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
4 1MQW - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1MR2 - A12 C11 H17 N5 O9 P2 c1nc(c2c(n....
2 1MK1 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
3 1MQE - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
4 1MQW - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: APR; Similar ligands found: 380
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 RBY 0.805195 0.958904
10 ADV 0.805195 0.958904
11 ATP 0.802632 0.971831
12 AN2 0.8 0.958333
13 AQP 0.792208 0.971831
14 5FA 0.792208 0.971831
15 AD9 0.782051 0.945205
16 AGS 0.782051 0.92
17 SAP 0.782051 0.92
18 ACP 0.779221 0.945205
19 AMP 0.753425 0.943662
20 A 0.753425 0.943662
21 3OD 0.747126 0.972222
22 PRX 0.746835 0.893333
23 OAD 0.744186 0.972222
24 CA0 0.74359 0.972222
25 ADX 0.74359 0.873418
26 ACQ 0.740741 0.945205
27 ANP 0.740741 0.945205
28 A22 0.738095 0.958333
29 50T 0.734177 0.931507
30 A2R 0.72619 0.985915
31 ABM 0.723684 0.917808
32 ATF 0.722892 0.932432
33 ADQ 0.72093 0.972222
34 A1R 0.72093 0.907895
35 AMP MG 0.710526 0.891892
36 AP2 0.705128 0.932432
37 A12 0.705128 0.932432
38 SRA 0.697368 0.893333
39 5AL 0.690476 0.958333
40 APC 0.682927 0.932432
41 ADP MG 0.679012 0.905405
42 AU1 0.679012 0.945205
43 TAT 0.678571 0.932432
44 SRP 0.674419 0.932432
45 ADP BEF 0.670732 0.881579
46 BEF ADP 0.670732 0.881579
47 BIS 0.67033 0.907895
48 25L 0.663043 0.958333
49 4AD 0.662921 0.945946
50 DLL 0.655556 0.958333
51 00A 0.655556 0.907895
52 ADP PO3 0.654762 0.943662
53 25A 0.651685 0.944444
54 OOB 0.651685 0.958333
55 5SV 0.651685 0.848101
56 8QN 0.651685 0.958333
57 ATP MG 0.647059 0.905405
58 AMO 0.644444 0.958904
59 PAJ 0.644444 0.909091
60 MAP 0.640449 0.92
61 OMR 0.64 0.875
62 AFH 0.639175 0.909091
63 AHX 0.637363 0.896104
64 FYA 0.634409 0.905405
65 3UK 0.630435 0.945205
66 NAX 0.63 0.873418
67 G3A 0.628866 0.896104
68 SON 0.626506 0.932432
69 ALF ADP 0.625 0.87013
70 ADP ALF 0.625 0.87013
71 WAQ 0.623656 0.907895
72 PR8 0.623656 0.873418
73 LAD 0.623656 0.884615
74 G5P 0.622449 0.896104
75 GAP 0.62069 0.918919
76 48N 0.62 0.921053
77 ANP MG 0.617977 0.894737
78 ADP VO4 0.617977 0.931507
79 VO4 ADP 0.617977 0.931507
80 AP0 0.617647 0.896104
81 ME8 0.617021 0.8625
82 NB8 0.617021 0.921053
83 1ZZ 0.617021 0.8625
84 PTJ 0.617021 0.896104
85 TXA 0.617021 0.958904
86 GTA 0.616162 0.8625
87 FA5 0.614583 0.932432
88 NAI 0.613861 0.907895
89 TXD 0.613861 0.907895
90 6V0 0.613861 0.896104
91 DND 0.613861 0.958904
92 NXX 0.613861 0.958904
93 TXE 0.607843 0.907895
94 9SN 0.604167 0.896104
95 UP5 0.598039 0.92
96 YAP 0.597938 0.92
97 XAH 0.591837 0.839506
98 XYA 0.589041 0.84507
99 RAB 0.589041 0.84507
100 ADN 0.589041 0.84507
101 DAL AMP 0.586957 0.931507
102 2A5 0.586207 0.893333
103 4UV 0.585859 0.92
104 AOC 0.585366 0.821918
105 ADJ 0.584906 0.875
106 7D4 0.581395 0.88
107 ITT 0.581395 0.916667
108 A4P 0.580952 0.821429
109 PAP 0.579545 0.957747
110 ATR 0.579545 0.943662
111 CNA 0.579439 0.932432
112 ADP BMA 0.578947 0.945205
113 5AS 0.576471 0.77907
114 4UU 0.574257 0.92
115 5N5 0.573333 0.819444
116 7D3 0.571429 0.88
117 4TC 0.571429 0.896104
118 T5A 0.570093 0.841463
119 139 0.570093 0.873418
120 COD 0.568807 0.811765
121 JB6 0.56701 0.883117
122 5CD 0.565789 0.805556
123 A4D 0.565789 0.819444
124 EP4 0.564103 0.753247
125 LAQ 0.563107 0.8625
126 NA7 0.5625 0.932432
127 TYM 0.561905 0.932432
128 YLP 0.557692 0.841463
129 A A 0.556701 0.917808
130 G5A 0.555556 0.77907
131 4UW 0.552381 0.884615
132 ATP A A A 0.55 0.930556
133 AVV 0.547368 0.896104
134 A3P 0.546512 0.943662
135 MYR AMP 0.545455 0.839506
136 7D5 0.54321 0.853333
137 G1R 0.542553 0.907895
138 UPA 0.542056 0.907895
139 YLB 0.542056 0.841463
140 YLC 0.542056 0.8625
141 NAD 0.540541 0.931507
142 AMP DBH 0.539216 0.918919
143 TAD 0.538462 0.884615
144 DTA 0.5375 0.786667
145 M2T 0.5375 0.734177
146 3DH 0.536585 0.773333
147 AYB 0.536364 0.831325
148 EAD 0.533898 0.873418
149 AHZ 0.533333 0.839506
150 FB0 0.532787 0.784091
151 IOT 0.53211 0.831325
152 A3D 0.530973 0.918919
153 MTA 0.530864 0.773333
154 3AM 0.53012 0.902778
155 TYR AMP 0.529412 0.906667
156 AR6 AR6 0.528846 0.944444
157 A2P 0.528736 0.929577
158 YLA 0.527273 0.841463
159 6AD 0.526882 0.884615
160 PPS 0.526882 0.85
161 BTX 0.526786 0.819277
162 NAE 0.525862 0.894737
163 BT5 0.522124 0.831325
164 A5A 0.521277 0.807229
165 TSB 0.520833 0.819277
166 6RE 0.517647 0.7375
167 P1H 0.516393 0.851852
168 3AT 0.516129 0.944444
169 SSA 0.515789 0.8
170 7MD 0.514286 0.886076
171 VMS 0.510417 0.788235
172 54H 0.510417 0.788235
173 52H 0.510417 0.77907
174 NSS 0.510204 0.8
175 NAQ 0.508475 0.871795
176 ZAS 0.505882 0.766234
177 IMO 0.505747 0.902778
178 A3N 0.505747 0.786667
179 J7C 0.505747 0.746835
180 AV2 0.505263 0.891892
181 53H 0.505155 0.77907
182 5CA 0.505155 0.8
183 ARU 0.50505 0.8375
184 ARG AMP 0.504673 0.829268
185 ALF ADP 3PG 0.504587 0.860759
186 AF3 ADP 3PG 0.504587 0.860759
187 LA8 ALF 3PG 0.504587 0.860759
188 YLY 0.504274 0.831325
189 ZID 0.504202 0.918919
190 2AM 0.5 0.916667
191 S4M 0.5 0.666667
192 DTP 0.5 0.88
193 FDA 0.5 0.811765
194 LPA AMP 0.5 0.839506
195 V3L 0.5 0.971831
196 FNK 0.496183 0.784091
197 6FA 0.496063 0.841463
198 DZD 0.495652 0.884615
199 P5A 0.49505 0.744444
200 LSS 0.494949 0.761364
201 DSZ 0.494949 0.821429
202 MAO 0.494382 0.759036
203 DSH 0.494253 0.725
204 M24 0.491525 0.873418
205 NJP 0.491228 0.92
206 NVA LMS 0.49 0.761364
207 DAT 0.48913 0.88
208 5X8 0.48913 0.786667
209 FAD 0.488372 0.851852
210 FAS 0.488372 0.851852
211 SFD 0.488372 0.734043
212 NAJ PZO 0.487179 0.848101
213 0WD 0.486957 0.896104
214 NPW 0.486726 0.8625
215 7MC 0.486486 0.864198
216 LEU LMS 0.485149 0.761364
217 7DT 0.483871 0.957747
218 7DD 0.483516 0.957747
219 GJV 0.483146 0.728395
220 OVE 0.482759 0.88
221 5AD 0.480519 0.746479
222 GSU 0.480392 0.8
223 KAA 0.480392 0.752809
224 NDE 0.48 0.906667
225 N0B 0.479339 0.841463
226 A5D 0.478723 0.786667
227 NAD IBO 0.478261 0.87013
228 ODP 0.478261 0.884615
229 RGT 0.47619 0.958904
230 XNP 0.474138 0.85
231 4TA 0.474138 0.807229
232 NDP 0.473684 0.896104
233 62F 0.473684 0.8625
234 SFG 0.473118 0.773333
235 NDC 0.472441 0.871795
236 YSA 0.471698 0.77907
237 ENP 0.470588 0.918919
238 FAY 0.470149 0.8625
239 TXP 0.469565 0.896104
240 NZQ 0.469565 0.884615
241 DDS 0.46875 0.853333
242 A7D 0.467391 0.776316
243 RFL 0.466667 0.821429
244 ENQ 0.466019 0.943662
245 AAT 0.463918 0.707317
246 SA8 0.463158 0.728395
247 7C5 0.462963 0.818182
248 MHZ 0.462366 0.697674
249 71V 0.461538 0.883117
250 G A A A 0.461538 0.848101
251 F2N 0.460993 0.793103
252 NEC 0.460674 0.746667
253 A3G 0.460674 0.8
254 GGZ 0.46 0.825
255 NAJ PYZ 0.459016 0.85
256 SAH 0.458333 0.766234
257 6C6 0.458333 0.857143
258 SAI 0.458333 0.75641
259 P5F 0.457143 0.823529
260 Y3J 0.45679 0.726027
261 A A A 0.456311 0.905405
262 PO4 PO4 A A A A PO4 0.456311 0.902778
263 7D7 0.455696 0.743243
264 SMM 0.454545 0.705882
265 V1N 0.453704 0.944444
266 6IA 0.453608 0.814815
267 SAM 0.453608 0.710843
268 WSA 0.451327 0.788235
269 EEM 0.44898 0.710843
270 PGS 0.446809 0.858974
271 DCA 0.446281 0.802326
272 ETB 0.446281 0.811765
273 U A G G 0.445378 0.858974
274 2SA 0.444444 0.932432
275 DA 0.444444 0.853333
276 D5M 0.444444 0.853333
277 AMP NAD 0.443548 0.906667
278 GP3 0.443299 0.896104
279 128 0.442478 0.776471
280 4YB 0.441441 0.781609
281 GEK 0.441176 0.759494
282 Z5A 0.44 0.77907
283 30N 0.44 0.734043
284 S7M 0.44 0.710843
285 AAM 0.43956 0.943662
286 0T1 0.439024 0.802326
287 COA 0.439024 0.802326
288 FA9 0.4375 0.841463
289 12D 0.4375 0.785714
290 AMZ 0.436782 0.890411
291 C2R 0.436782 0.90411
292 A3S 0.43617 0.810811
293 N6P 0.432692 0.888889
294 PUA 0.430894 0.860759
295 PLP AAD 0.429752 0.741573
296 AMX 0.428571 0.811765
297 AIR 0.428571 0.875
298 TAP 0.428571 0.883117
299 1DG 0.428571 0.896104
300 A6D 0.428571 0.722892
301 DG1 0.428571 0.896104
302 COS 0.428571 0.784091
303 CAO 0.428571 0.775281
304 6K6 0.427184 0.90411
305 A3T 0.427083 0.821918
306 NIA 0.426966 0.8
307 649 0.426087 0.744444
308 GTP 0.425743 0.894737
309 CMX 0.425197 0.823529
310 SCO 0.425197 0.823529
311 G2R 0.424528 0.860759
312 GDP 0.424242 0.894737
313 7RA 0.423913 0.930556
314 0UM 0.423077 0.719512
315 OXK 0.423077 0.804598
316 ACO 0.421875 0.775281
317 FCX 0.421875 0.795455
318 FAM 0.421875 0.784091
319 GCP 0.421569 0.871795
320 NAP 0.420635 0.918919
321 SXZ 0.420561 0.731707
322 GNH 0.42 0.883117
323 62X 0.419048 0.686047
324 APU 0.418803 0.87013
325 A U 0.418803 0.87013
326 HAX 0.418605 0.784091
327 GDD 0.418182 0.884615
328 GKE 0.418182 0.884615
329 GDC 0.418182 0.884615
330 101 0.417582 0.853333
331 GSP 0.417476 0.85
332 2MC 0.416667 0.75
333 3AD 0.416667 0.805556
334 FYN 0.415385 0.802326
335 3KK 0.415385 0.784091
336 G2Q 0.415094 0.860759
337 K15 0.415094 0.702381
338 NA0 0.414062 0.906667
339 IVC 0.413534 0.793103
340 S8M 0.413462 0.759494
341 NHD 0.413223 0.905405
342 7RP 0.413043 0.901408
343 COK 0.412214 0.784091
344 CA6 0.412214 0.71134
345 MCD 0.412214 0.804598
346 SOP 0.412214 0.784091
347 NMX 0.409091 0.741935
348 CMC 0.409091 0.804598
349 1VU 0.409091 0.775281
350 CO6 0.409091 0.784091
351 AS 0.408602 0.810127
352 CNV FAD 0.408451 0.772727
353 ACK 0.406593 0.861111
354 QQY 0.406593 0.815789
355 6YU 0.40625 0.734043
356 SCD 0.406015 0.823529
357 CAJ 0.406015 0.804598
358 NAD BBN 0.405797 0.841463
359 8BR 0.404255 0.881579
360 GNP 0.403846 0.871795
361 APX 0.40367 0.907895
362 TM1 0.40367 0.77381
363 KB1 0.40367 0.719512
364 SLU 0.403226 0.770115
365 3HC 0.402985 0.793103
366 1HE 0.402985 0.766667
367 MLC 0.402985 0.804598
368 BCO 0.402985 0.784091
369 A1S 0.402985 0.784091
370 1CZ 0.402878 0.795455
371 CC5 0.402439 0.816901
372 NMN AMP PO4 0.401639 0.87013
373 FAQ 0.40146 0.784091
374 CAA 0.4 0.793103
375 COO 0.4 0.784091
376 2BA 0.4 0.915493
377 MCA 0.4 0.795455
378 YE1 0.4 0.793103
379 CMP 0.4 0.901408
380 NAD CJ3 0.4 0.811765
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MK1; Ligand: APR; Similar sites found: 70
This union binding pocket(no: 1) in the query (biounit: 1mk1.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.003135 0.48136 None
2 3UEC ALA ARG TPO LYS 0.002104 0.45448 None
3 1UO4 PIH 0.01394 0.4366 None
4 4DXG NDG FUC SIA GAL 0.01874 0.41406 None
5 2VKL MLT 0.03713 0.4138 None
6 2B7N NTM 0.01059 0.41035 None
7 3GM5 CIT 0.005166 0.42983 1.88679
8 3BY8 MLT 0.01016 0.42242 2.8169
9 1JN2 SFP 0.01424 0.4699 2.89855
10 3BHO B4P 0.02119 0.42688 2.89855
11 2ZJ5 ADP 0.009631 0.41215 2.89855
12 3U1T MLI 0.01732 0.4115 2.89855
13 2IZ1 ATR 0.01556 0.40814 2.89855
14 2RDG NDG FUC SIA GAL 0.03125 0.40147 3.06122
15 1DXY COI 0.003227 0.46127 3.38164
16 1I0Z OXM 0.0189 0.42221 3.38164
17 2CUN 3PG 0.03083 0.40384 3.38164
18 2EB5 OXL 0.02243 0.40091 3.38164
19 2XG5 EC5 0.02174 0.42082 3.46821
20 3R51 MMA 0.01314 0.43026 3.75
21 1MZV AMP 0.0005126 0.44847 3.86473
22 2ZWS PLM 0.02867 0.42768 3.86473
23 4JEJ 1GP 0.005028 0.40479 3.86473
24 3GTD MLI 0.01626 0.40218 3.86473
25 3P3N AKG 0.02176 0.40151 3.86473
26 3KMT SAH 0.004185 0.40356 4.20168
27 1Y75 NAG 0.0108 0.40039 4.23729
28 1Y7P RIP 0.03227 0.40421 4.34783
29 4B9E FAH 0.01196 0.41908 4.65116
30 4M5P 23W 0.006055 0.43982 4.83092
31 4M5P MLA 0.01233 0.43943 4.83092
32 2JBH 5GP 0.003134 0.42236 4.83092
33 2VAR AMP 0.002945 0.41844 4.83092
34 1XX4 BAM 0.02818 0.41331 4.83092
35 1ZCH FMN 0.001169 0.40321 4.83092
36 4F4S EFO 0.01414 0.40005 5.26316
37 1V5F TPP 0.02366 0.41883 5.31401
38 1V5F FAD 0.02366 0.41883 5.31401
39 2Q1A 2KT 0.01185 0.4135 5.31401
40 1ULE GLA GAL NAG 0.004695 0.4452 5.33333
41 4F8L GAL 0.02497 0.43106 5.51724
42 1YOA FMN 0.00525 0.4689 5.66038
43 3E5P PPI 0.003975 0.49144 5.7971
44 1YHM AHD 0.01385 0.40524 5.7971
45 3IU9 T07 0.009752 0.40428 5.7971
46 3F81 STT 0.03065 0.41144 6.01093
47 3BRE C2E 0.009233 0.41842 6.28019
48 1W3R PYR 0.01609 0.41907 7.24638
49 3LTW HLZ 0.009167 0.41856 7.24638
50 3TFC PEP 0.01363 0.40073 7.24638
51 4NAO AKG 0.007341 0.42904 7.72947
52 2V5E SCR 0.0112 0.44166 7.92079
53 1NU4 MLA 0.002101 0.48024 8.24742
54 3GJB AKG 0.003127 0.4224 8.69565
55 3O2K DST 0.01289 0.40176 8.69565
56 4JCA CIT 0.01811 0.43052 8.98204
57 3RF4 FUN 0.01227 0.40266 9.48276
58 2QLX RM4 0.01331 0.4169 10.1852
59 3F8C HT1 0.0172 0.40111 10.3175
60 3MAG 3MA 0.002625 0.47511 11.1111
61 1G8S MET 0.01865 0.40456 11.5942
62 1O9U ADZ 0.003046 0.46254 12.0773
63 1Q11 TYE 0.005885 0.41616 13.0435
64 1Z44 NPO 0.01876 0.43803 13.5266
65 2XVE FAD 0.006095 0.41386 14.0097
66 2NVK NAP 0.003932 0.42355 14.4928
67 2O1C PPV 0.00008412 0.48135 14.6667
68 4RJK PYR 0.0102 0.42876 16.9082
69 3O61 GDD 0.0001409 0.46585 23.0366
70 2YVO AMP 0.000005202 0.52473 37.3626
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