Receptor
PDB id Resolution Class Description Source Keywords
2PKN 1.9 Å EC: 2.7.1.20 CRYSTAL STRUCTURE OF M TUBERCULOSIS ADENOSINE KINASE COMPLEX AMP-PCP (NON-HYDROLYZABLE ATP ANALOG) MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE TRANSFERASE SGENOMICS TB STRUCTURAL GENOMICS CONSORTIUM TBSGC
Ref.: HIGH RESOLUTION CRYSTAL STRUCTURES OF MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE: INSIGHTS INTO THE ME AND SPECIFICITY OF THIS NOVEL PROKARYOTIC ENZYME J.BIOL.CHEM. V. 282 27334 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACP A:325;
Valid;
none;
submit data
505.208 C11 H18 N5 O12 P3 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C9V 1.7 Å EC: 2.7.1.20 MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE BOUND TO (2R,3S, (HYDROXYMETHYL)-5-(6-(4-PHENYLPIPERAZIN-1-YL)-9H-PURIN-9-YLT ETRAHYDROFURAN-3,4-DIOL MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE ANALOG COMPLEX INHIBITOR STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE TB STRUCTURAL GENOMICS CONSORTBSGC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DRUG DESIGN OF 6-SUBSTITUTED ADENO ANALOGUES AS POTENT INHIBITORS OF MYCOBACTERIUM TUB ADENOSINE KINASE. J.MED.CHEM. V. 62 4483 2019
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
13 3B1P - NOS C10 H12 N4 O5 c1nc2c(n1[....
14 3B1Q - NOS C10 H12 N4 O5 c1nc2c(n1[....
15 3B1R - AMP MG n/a n/a
16 3B1N - MZR C9 H13 N3 O6 c1nc(c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ACP; Similar ligands found: 391
No: Ligand ECFP6 Tc MDL keys Tc
1 ACP 1 1
2 ACQ 0.866667 1
3 A2D 0.857143 0.945205
4 BA3 0.833333 0.945205
5 6YZ 0.833333 1
6 B4P 0.821918 0.945205
7 AP5 0.821918 0.945205
8 ADP 0.821918 0.972222
9 AT4 0.810811 0.933333
10 AN2 0.810811 0.958904
11 A12 0.808219 0.986301
12 AP2 0.808219 0.986301
13 M33 0.8 0.932432
14 HEJ 0.789474 0.972222
15 ATP 0.789474 0.972222
16 AQP 0.779221 0.972222
17 5FA 0.779221 0.972222
18 AR6 0.779221 0.945205
19 APR 0.779221 0.945205
20 AGS 0.769231 0.921053
21 AD9 0.769231 0.945946
22 SAP 0.769231 0.921053
23 AMP 0.763889 0.944444
24 A 0.763889 0.944444
25 APC 0.75641 0.986301
26 ADX 0.753247 0.851852
27 CA0 0.753247 0.92
28 ANP 0.75 0.945946
29 50T 0.74359 0.932432
30 KG4 0.74359 0.92
31 PRX 0.734177 0.87013
32 45A 0.733333 0.893333
33 ABM 0.733333 0.893333
34 ATF 0.731707 0.933333
35 HQG 0.714286 0.958904
36 SRA 0.706667 0.894737
37 A22 0.705882 0.958904
38 RBY 0.703704 0.959459
39 ADV 0.703704 0.959459
40 8LE 0.698795 0.871795
41 5AL 0.698795 0.906667
42 ADP MG 0.696203 0.917808
43 ADQ 0.689655 0.92
44 A1R 0.689655 0.909091
45 A3R 0.689655 0.909091
46 AU1 0.6875 0.945946
47 T99 0.686747 0.933333
48 TAT 0.686747 0.933333
49 APC MG 0.682927 0.918919
50 SRP 0.682353 0.907895
51 8LH 0.682353 0.883117
52 9X8 0.674157 0.896104
53 OAD 0.674157 0.92
54 4TC 0.673469 0.922078
55 4AD 0.670455 0.921053
56 AMO 0.670455 0.933333
57 8LQ 0.666667 0.907895
58 00A 0.662921 0.860759
59 ATP MG 0.662651 0.917808
60 ADP PO3 0.662651 0.917808
61 BIS 0.659341 0.909091
62 3OD 0.659341 0.92
63 OZV 0.659091 0.945205
64 25A 0.659091 0.945205
65 OOB 0.659091 0.906667
66 8QN 0.659091 0.906667
67 5SV 0.659091 0.82716
68 SON 0.654321 0.933333
69 25L 0.652174 0.958904
70 PAJ 0.651685 0.8625
71 DLL 0.644444 0.906667
72 AHX 0.644444 0.897436
73 TXA 0.641304 0.907895
74 3UK 0.637363 0.894737
75 ADP ALF 0.632184 0.848101
76 ALF ADP 0.632184 0.848101
77 B5V 0.630435 0.883117
78 PR8 0.630435 0.851852
79 WAQ 0.630435 0.884615
80 LAD 0.630435 0.8625
81 MAP 0.629214 0.921053
82 LMS 0.628205 0.807229
83 GAP 0.627907 0.87013
84 ADP VO4 0.625 0.906667
85 VO4 ADP 0.625 0.906667
86 PTJ 0.623656 0.873418
87 ME8 0.623656 0.841463
88 NB8 0.623656 0.897436
89 FYA 0.623656 0.906667
90 1ZZ 0.623656 0.819277
91 UP5 0.62 0.896104
92 G3A 0.618557 0.897436
93 G5P 0.612245 0.897436
94 AFH 0.612245 0.886076
95 9SN 0.610526 0.85
96 GTA 0.606061 0.864198
97 DQV 0.606061 0.932432
98 9ZA 0.604396 0.884615
99 9ZD 0.604396 0.884615
100 YAP 0.604167 0.896104
101 B5M 0.604167 0.871795
102 FA5 0.604167 0.907895
103 B5Y 0.604167 0.871795
104 TXD 0.60396 0.884615
105 XAH 0.597938 0.841463
106 RAB 0.597222 0.821918
107 ADN 0.597222 0.821918
108 XYA 0.597222 0.821918
109 GA7 0.59596 0.907895
110 48N 0.594059 0.897436
111 DAL AMP 0.593407 0.881579
112 2A5 0.593023 0.92
113 AOC 0.592593 0.8
114 4UV 0.591837 0.871795
115 NAI 0.588235 0.884615
116 DND 0.588235 0.907895
117 NXX 0.588235 0.907895
118 NAX 0.588235 0.875
119 6V0 0.588235 0.873418
120 ATR 0.586207 0.944444
121 PAP 0.586207 0.958333
122 ADP BMA 0.585106 0.894737
123 LAQ 0.584158 0.819277
124 5AS 0.583333 0.761364
125 OMR 0.582524 0.831325
126 TXE 0.582524 0.884615
127 5N5 0.581081 0.797297
128 4UU 0.58 0.871795
129 A A 0.578947 0.918919
130 7D3 0.578313 0.881579
131 AP0 0.576923 0.873418
132 5CD 0.573333 0.783784
133 A4D 0.573333 0.797297
134 JB6 0.572917 0.884615
135 4UW 0.572816 0.839506
136 A4P 0.571429 0.823529
137 CNA 0.570093 0.907895
138 7D4 0.569767 0.881579
139 ITT 0.569767 0.917808
140 A2R 0.565217 0.958904
141 M2T 0.564103 0.716049
142 YLP 0.563107 0.821429
143 139 0.560748 0.851852
144 ADJ 0.560748 0.831325
145 T5A 0.560748 0.843373
146 TAD 0.558824 0.910256
147 ATP A 0.555556 0.905405
148 ATP A A A 0.555556 0.905405
149 A3P 0.552941 0.944444
150 TYM 0.552381 0.907895
151 IOT 0.551402 0.833333
152 EP4 0.551282 0.734177
153 MYR AMP 0.55102 0.797619
154 F2R 0.550459 0.865854
155 7D5 0.55 0.855263
156 A3D 0.54955 0.894737
157 80F 0.54955 0.843373
158 GCP 0.548387 0.922078
159 YLB 0.54717 0.821429
160 YLC 0.54717 0.841463
161 UPA 0.54717 0.884615
162 NAD 0.545455 0.906667
163 H1Q 0.545455 0.88
164 COD 0.545455 0.813953
165 JSQ 0.544444 0.921053
166 HFD 0.544444 0.921053
167 G5A 0.544444 0.781609
168 DTA 0.544304 0.766234
169 3DH 0.54321 0.753247
170 DZD 0.540541 0.910256
171 AHZ 0.538462 0.797619
172 MTA 0.5375 0.753247
173 3AM 0.536585 0.90411
174 A2P 0.534884 0.930556
175 AR6 AR6 0.533981 0.893333
176 PPS 0.532609 0.851852
177 6AD 0.532609 0.886076
178 YLA 0.53211 0.821429
179 AMP DBH 0.529412 0.87013
180 TYR AMP 0.529412 0.871795
181 AYB 0.527273 0.811765
182 A5A 0.526882 0.788235
183 TSB 0.526316 0.8
184 6RE 0.52381 0.7625
185 S4M 0.523256 0.670455
186 SSA 0.521277 0.802326
187 NA7 0.520408 0.959459
188 ARG AMP 0.519231 0.831325
189 7MD 0.519231 0.864198
190 LPA AMP 0.518868 0.797619
191 BTX 0.517857 0.843373
192 NAE 0.517241 0.871795
193 NO7 0.515789 0.907895
194 VMS 0.515789 0.770115
195 52H 0.515789 0.761364
196 54H 0.515789 0.770115
197 BT5 0.513274 0.833333
198 NAQ 0.512821 0.85
199 ZAS 0.511905 0.746835
200 IMO 0.511628 0.90411
201 J7C 0.511628 0.772152
202 A3N 0.511628 0.766234
203 AV2 0.510638 0.893333
204 53H 0.510417 0.761364
205 8X1 0.510417 0.755556
206 5CA 0.510417 0.802326
207 ARU 0.510204 0.839506
208 AF3 ADP 3PG 0.509259 0.839506
209 M24 0.508621 0.829268
210 ZID 0.508475 0.894737
211 2AM 0.506024 0.917808
212 6MZ 0.505747 0.905405
213 3AT 0.505376 0.972222
214 V3L 0.505376 0.945205
215 AVV 0.505155 0.897436
216 NSS 0.5 0.802326
217 MAO 0.5 0.761905
218 P5A 0.5 0.747253
219 EAD 0.5 0.851852
220 DSH 0.5 0.728395
221 DSZ 0.5 0.802326
222 LSS 0.5 0.764045
223 YLY 0.495726 0.811765
224 9K8 0.49505 0.698925
225 NVA LMS 0.494949 0.755556
226 DAT 0.494505 0.906667
227 5X8 0.494505 0.766234
228 AMP NAD 0.491228 0.881579
229 7MC 0.490909 0.843373
230 LEU LMS 0.49 0.755556
231 SMM 0.489583 0.689655
232 SAM 0.489362 0.694118
233 DTP 0.489362 0.906667
234 7DD 0.488889 0.958333
235 GJV 0.488636 0.753086
236 OVE 0.488372 0.881579
237 5AD 0.486842 0.726027
238 KAA 0.485149 0.755556
239 GSU 0.485149 0.781609
240 NDE 0.483871 0.907895
241 P1H 0.483871 0.831325
242 N0B 0.483333 0.821429
243 A3G 0.482759 0.802632
244 NAJ PZO 0.478632 0.82716
245 4TA 0.478261 0.809524
246 SFG 0.478261 0.753247
247 YSA 0.47619 0.781609
248 FB0 0.47619 0.827586
249 NDC 0.47619 0.85
250 7DT 0.473118 0.958333
251 A7D 0.472527 0.779221
252 J4G 0.470588 0.921053
253 NJP 0.469565 0.921053
254 FDA 0.46875 0.835294
255 SA8 0.468085 0.710843
256 A5D 0.468085 0.766234
257 MHZ 0.467391 0.701149
258 8PZ 0.466667 0.802326
259 71V 0.466667 0.884615
260 G A A A 0.465517 0.85
261 0WD 0.465517 0.897436
262 6FA 0.465116 0.843373
263 GGZ 0.464646 0.804878
264 SAH 0.463158 0.746835
265 6C6 0.463158 0.883117
266 SAI 0.463158 0.7375
267 NAJ PYZ 0.46281 0.788235
268 Y3J 0.4625 0.706667
269 B1U 0.462264 0.72043
270 LQJ 0.462264 0.893333
271 7D7 0.461538 0.723684
272 TXP 0.46087 0.897436
273 PO4 PO4 A A A A PO4 0.460784 0.878378
274 S7M 0.459184 0.694118
275 DDS 0.458333 0.855263
276 6IA 0.458333 0.839506
277 FAD 0.458015 0.853659
278 FAS 0.458015 0.853659
279 SFD 0.458015 0.736842
280 ODP 0.456897 0.886076
281 A3S 0.456522 0.813333
282 U A 0.453782 0.884615
283 7C5 0.453704 0.797468
284 EEM 0.453608 0.694118
285 AAT 0.453608 0.710843
286 A G 0.452991 0.860759
287 RGT 0.45283 0.933333
288 NPW 0.452174 0.8875
289 NDP 0.452174 0.897436
290 FAY 0.451852 0.864198
291 PGS 0.451613 0.860759
292 KOY 0.45045 0.782051
293 NEC 0.449438 0.727273
294 DA 0.449438 0.88
295 D5M 0.449438 0.88
296 U A G G 0.449153 0.860759
297 2SA 0.44898 0.933333
298 NIA 0.448276 0.802469
299 NZQ 0.448276 0.910256
300 A U 0.447368 0.848101
301 A3T 0.446809 0.8
302 A A A 0.446602 0.906667
303 128 0.446429 0.758621
304 6K6 0.445545 0.905405
305 GEK 0.445545 0.740741
306 4YB 0.445455 0.764045
307 FNK 0.444444 0.806818
308 62F 0.444444 0.864198
309 AAM 0.444444 0.944444
310 Z5A 0.443548 0.761364
311 WSA 0.442478 0.790698
312 C2R 0.44186 0.88
313 AMZ 0.44186 0.891892
314 12D 0.441441 0.767442
315 XNP 0.440678 0.851852
316 RFL 0.437956 0.823529
317 62X 0.436893 0.670455
318 N6P 0.436893 0.890411
319 AIR 0.433735 0.876712
320 N5O 0.433333 0.766234
321 GP3 0.43299 0.897436
322 A6D 0.432692 0.705882
323 V1N 0.431193 0.893333
324 649 0.429825 0.747253
325 GP2 0.428571 0.910256
326 GDP 0.428571 0.896104
327 NA0 0.428571 0.907895
328 0UM 0.427184 0.702381
329 DCA 0.42623 0.825581
330 ETB 0.42623 0.835294
331 8Q2 0.426087 0.775281
332 9JJ 0.425532 0.841463
333 GNH 0.424242 0.884615
334 NAP 0.424 0.92
335 N5A 0.423913 0.74026
336 PUA 0.422764 0.8625
337 APU 0.422414 0.871795
338 101 0.422222 0.855263
339 3AD 0.421687 0.808219
340 FA9 0.42069 0.865854
341 TAP 0.420635 0.884615
342 TM1 0.420561 0.755814
343 P5F 0.41958 0.825581
344 0T1 0.419355 0.825581
345 COA 0.419355 0.825581
346 K15 0.419048 0.686047
347 7RP 0.417582 0.902778
348 S8M 0.417476 0.7625
349 NHD 0.416667 0.881579
350 GTP 0.415842 0.896104
351 FCX 0.414062 0.797753
352 F2N 0.413793 0.816092
353 AS 0.413043 0.835443
354 7RA 0.413043 0.931507
355 G1R 0.411765 0.884615
356 SXZ 0.411215 0.714286
357 ACK 0.411111 0.837838
358 QQY 0.411111 0.794872
359 J7V 0.409449 0.813953
360 COS 0.409449 0.806818
361 30N 0.409449 0.755319
362 1DG 0.409449 0.897436
363 DG1 0.409449 0.897436
364 AMX 0.409449 0.835294
365 CAO 0.409449 0.797753
366 EO7 0.408602 0.770115
367 8BR 0.408602 0.883117
368 9BG 0.408333 0.873418
369 NVA 2AD 0.408163 0.7625
370 D3Y 0.407767 0.792208
371 9GM 0.407767 0.873418
372 G2P 0.407767 0.910256
373 GNP 0.407767 0.873418
374 GSP 0.407767 0.851852
375 KB1 0.407407 0.702381
376 CC5 0.407407 0.819444
377 A C A C 0.406504 0.82716
378 N01 0.406504 0.881579
379 CMX 0.40625 0.825581
380 SCO 0.40625 0.825581
381 HDV 0.405941 0.87013
382 CMP 0.404255 0.876712
383 2BA 0.404255 0.890411
384 ACO 0.403101 0.797753
385 FAM 0.403101 0.806818
386 2VA 0.402062 0.779221
387 3NZ 0.401869 0.78481
388 HAX 0.4 0.806818
389 26A 0.4 0.74359
390 QQX 0.4 0.78481
391 OZP 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C9V; Ligand: ERS; Similar sites found with APoc: 17
This union binding pocket(no: 1) in the query (biounit: 6c9v.bio1) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 2VAR AMP 6.70927
2 2VAR AMP 6.70927
3 2VAR AMP 6.70927
4 2VAR ANP 6.70927
5 2VAR ANP 6.70927
6 2VAR ANP 6.70927
7 6ILS ATP 8.6262
8 6ILS ATP 8.6262
9 2HW1 FRU 8.72483
10 6A8A ATP 32.4074
11 6A8A ATP 32.4074
12 1V1A ADP 36.8932
13 4XDA ADP 39.1586
14 4XDA ADP 39.1586
15 2C49 ANP 43.0464
16 2C49 ADN 43.0464
17 2C49 ANP 43.0464
Pocket No.: 2; Query (leader) PDB : 6C9V; Ligand: ERS; Similar sites found with APoc: 17
This union binding pocket(no: 2) in the query (biounit: 6c9v.bio1) has 70 residues
No: Leader PDB Ligand Sequence Similarity
1 2VAR AMP 6.70927
2 2VAR AMP 6.70927
3 2VAR AMP 6.70927
4 2VAR ANP 6.70927
5 2VAR ANP 6.70927
6 2VAR ANP 6.70927
7 6ILS ATP 8.6262
8 6ILS ATP 8.6262
9 2HW1 FRU 8.72483
10 6A8A ATP 32.4074
11 6A8A ATP 32.4074
12 1V1A ADP 36.8932
13 4XDA ADP 39.1586
14 4XDA ADP 39.1586
15 2C49 ANP 43.0464
16 2C49 ADN 43.0464
17 2C49 ANP 43.0464
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