Receptor
PDB id Resolution Class Description Source Keywords
1DVR 2.36 Å EC: 2.7.4.3 STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-A SHOWING DOMAIN CLOSURE OVER ATP SACCHAROMYCES CEREVISIAE NUCLEOSIDE MONOPHOSPHATE KINASE MYOKINASE TRANSFERASE (PHOSPHOTRANSFERASE)
Ref.: STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP. J.MOL.BIOL. V. 256 223 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ATF A:230;
B:230;
 Valid;
Valid;
 none;
none;
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541.189 C11 H16 F2 N5 O12 P3 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1AKY 1.63 Å EC: 2.7.4.3 HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF P HOSPHORYL TRANSFER SACCHAROMYCES CEREVISIAE ATP:AMP PHOSPHOTRANSFERASE MYOKINASE TRANSFERASE (PHOSPHOTRANSFERASE)
Ref.: HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER. PROTEIN SCI. V. 4 1262 1995
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
2 1DVR - ATF C11 H16 F2 N5 O12 P3 c1nc(c2c(n....
3 3AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
4 2AKY - AP5 C20 H29 N10 O22 P5 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 10 families.
1 1AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
2 1DVR - ATF C11 H16 F2 N5 O12 P3 c1nc(c2c(n....
3 3AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
4 2AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
50% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
2 1DVR - ATF C11 H16 F2 N5 O12 P3 c1nc(c2c(n....
3 3AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
4 2AKY - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
5 1P3J - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
6 2EU8 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
7 4MKF - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
8 1E4Y - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
9 3HPR - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
10 6F7U - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
11 1E4V - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
12 4X8L - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
13 1AKE - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
14 3HPQ - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
15 1ANK - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 4X8O Kd = 250 nM AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
17 5G40 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 5G3Z - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
19 5G41 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
20 2RGX - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
21 4UKD - UDP ADP BF2 n/a n/a
22 5UKD - AF3 Al F3 F[Al](F)F
23 1QF9 - ALF Al F4 F[Al-](F)(....
24 2UKD - C5P C9 H14 N3 O8 P C1=CN(C(=O....
25 1S3G - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
26 3FB4 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
27 6ZJE - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
28 2AK3 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
29 6ZJB - G5P C20 H29 N10 O23 P5 c1nc(c2c(n....
30 6ZJD Kd = 13 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
31 4MKG - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
32 4MKH - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
33 5G3Y - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 1UKY - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
35 1UKZ - AMP C10 H14 N5 O7 P c1nc(c2c(n....
36 2BWJ - AMP C10 H14 N5 O7 P c1nc(c2c(n....
37 1ZIP - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
38 1ZIO - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
39 1ZIN - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
40 1Z83 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
41 4W5J - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
42 4NU0 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
43 2CDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ATF; Similar ligands found: 385
No: Ligand ECFP6 Tc MDL keys Tc
1 ATF 1 1
2 A2D 0.789474 0.932432
3 BA3 0.769231 0.932432
4 B4P 0.759494 0.932432
5 AP5 0.759494 0.932432
6 ADP 0.759494 0.958904
7 AN2 0.75 0.945946
8 AT4 0.75 0.921053
9 BIS 0.744444 0.973333
10 M33 0.740741 0.92
11 ACP 0.731707 0.933333
12 HEJ 0.731707 0.958904
13 ATP 0.731707 0.958904
14 AQP 0.722892 0.958904
15 5FA 0.722892 0.958904
16 APR 0.722892 0.932432
17 AR6 0.722892 0.932432
18 ANP 0.717647 0.933333
19 AGS 0.714286 0.909091
20 AD9 0.714286 0.933333
21 A 0.705128 0.931507
22 AMP 0.705128 0.931507
23 HQG 0.704545 0.945946
24 ADX 0.698795 0.841463
25 CA0 0.698795 0.907895
26 ACQ 0.697674 0.933333
27 50T 0.690476 0.92
28 KG4 0.690476 0.907895
29 PRX 0.682353 0.858974
30 ABM 0.679012 0.881579
31 45A 0.679012 0.881579
32 AMP MG 0.675 0.891892
33 6YZ 0.674157 0.933333
34 8LE 0.670455 0.860759
35 ADQ 0.663043 0.907895
36 A12 0.662651 0.921053
37 AP2 0.662651 0.921053
38 A22 0.659341 0.945946
39 SRA 0.654321 0.883117
40 5AL 0.651685 0.894737
41 ADP MG 0.647059 0.905405
42 ADP BEF 0.647059 0.905405
43 A3R 0.645161 0.873418
44 A1R 0.645161 0.873418
45 APC 0.643678 0.921053
46 TAT 0.640449 0.921053
47 T99 0.640449 0.921053
48 AU1 0.639535 0.933333
49 JNT 0.638298 0.907895
50 SRP 0.637363 0.871795
51 8LH 0.637363 0.871795
52 5SV 0.634409 0.817073
53 OZV 0.634409 0.932432
54 OAD 0.631579 0.907895
55 9X8 0.631579 0.884615
56 PAJ 0.62766 0.851852
57 8LQ 0.623656 0.871795
58 QA7 0.623656 0.860759
59 00A 0.621053 0.897436
60 AHX 0.621053 0.8625
61 3OD 0.618557 0.907895
62 APC MG 0.617977 0.881579
63 RBY 0.617977 0.896104
64 ATP MG 0.617977 0.905405
65 ADV 0.617977 0.896104
66 ADP PO3 0.617977 0.905405
67 25A 0.617021 0.932432
68 8QN 0.617021 0.894737
69 OOB 0.617021 0.894737
70 25L 0.612245 0.945946
71 BEF ADP 0.611111 0.881579
72 AMO 0.610526 0.896104
73 4AD 0.610526 0.884615
74 ALF ADP 0.608696 0.909091
75 LAD 0.608247 0.829268
76 PR8 0.608247 0.819277
77 MAP 0.606383 0.909091
78 9SN 0.606061 0.910256
79 DLL 0.604167 0.894737
80 PTJ 0.602041 0.8625
81 1ZZ 0.602041 0.809524
82 KMQ 0.6 0.896104
83 G3A 0.598039 0.886076
84 3UK 0.597938 0.883117
85 V2G 0.597826 0.8625
86 AFH 0.592233 0.923077
87 G5P 0.592233 0.886076
88 WAQ 0.591837 0.85
89 B5V 0.591837 0.871795
90 ANP MG 0.591398 0.894737
91 VO4 ADP 0.591398 0.907895
92 SON 0.590909 0.896104
93 GAP 0.586957 0.858974
94 GTA 0.586538 0.853659
95 TXA 0.585859 0.896104
96 NB8 0.585859 0.8625
97 ME8 0.585859 0.809524
98 FYA 0.585859 0.87013
99 UP5 0.584906 0.884615
100 B5M 0.584158 0.860759
101 LMS 0.583333 0.797619
102 XAH 0.578431 0.809524
103 GA7 0.576923 0.871795
104 4TC 0.574074 0.8625
105 4UV 0.572816 0.860759
106 DQV 0.571429 0.92
107 NAX 0.570093 0.841463
108 6V0 0.570093 0.8625
109 FA5 0.568627 0.871795
110 B5Y 0.568627 0.860759
111 9ZA 0.56701 0.873418
112 9ZD 0.56701 0.873418
113 ADP BMA 0.565657 0.883117
114 OMR 0.564815 0.821429
115 4UU 0.561905 0.860759
116 48N 0.560748 0.8625
117 AP0 0.559633 0.8625
118 L3W 0.559633 0.896104
119 139 0.558559 0.841463
120 DAL AMP 0.556701 0.87013
121 DND 0.555556 0.896104
122 TXD 0.555556 0.873418
123 ARU 0.555556 0.875
124 NAI 0.555556 0.873418
125 A4P 0.554545 0.813953
126 2A5 0.554348 0.883117
127 AOC 0.551724 0.789474
128 XYA 0.551282 0.810811
129 RAB 0.551282 0.810811
130 ADN 0.551282 0.810811
131 TXE 0.550459 0.873418
132 PAP 0.548387 0.945205
133 ATR 0.548387 0.931507
134 UPA 0.545455 0.873418
135 T5A 0.544643 0.811765
136 5AS 0.544444 0.752809
137 COD 0.54386 0.784091
138 4UW 0.541284 0.829268
139 7D3 0.539326 0.87013
140 JB6 0.539216 0.85
141 5N5 0.5375 0.786667
142 LAQ 0.537037 0.809524
143 MYR AMP 0.533981 0.788235
144 ITT 0.532609 0.905405
145 7D4 0.532609 0.87013
146 YLP 0.53211 0.790698
147 ADJ 0.530973 0.821429
148 5CD 0.530864 0.797297
149 A4D 0.530864 0.786667
150 A2R 0.530612 0.945946
151 JSQ 0.526316 0.986486
152 CNA 0.526316 0.896104
153 HFD 0.526316 0.986486
154 ATP A 0.52381 0.893333
155 ATP A A A 0.52381 0.893333
156 6RE 0.522727 0.731707
157 TYM 0.522523 0.871795
158 IOT 0.522124 0.802326
159 F2R 0.521739 0.833333
160 80F 0.521368 0.811765
161 AR6 AR6 0.518519 0.881579
162 YLB 0.517857 0.790698
163 YLC 0.517857 0.809524
164 BTX 0.517241 0.811765
165 NAD 0.517241 0.894737
166 3AM 0.517241 0.891892
167 A3P 0.516484 0.931507
168 BT5 0.512821 0.802326
169 EP4 0.511905 0.725
170 7D5 0.511628 0.844156
171 H1Q 0.510638 0.868421
172 G5A 0.510417 0.752809
173 A3D 0.508475 0.883117
174 M2T 0.505882 0.707317
175 DTA 0.505882 0.75641
176 3DH 0.505747 0.74359
177 SSA 0.50505 0.772727
178 ARG AMP 0.504587 0.8
179 YLA 0.504348 0.790698
180 AMP DBH 0.5 0.858974
181 MTA 0.5 0.74359
182 A2P 0.5 0.917808
183 6AD 0.5 0.875
184 PPS 0.5 0.841463
185 TAD 0.5 0.851852
186 52H 0.5 0.752809
187 AYB 0.5 0.781609
188 AF3 ADP 3PG 0.495575 0.875
189 ALF ADP 3PG 0.495575 0.875
190 AHZ 0.495495 0.788235
191 TSB 0.49505 0.790698
192 53H 0.49505 0.752809
193 A5A 0.494949 0.77907
194 J7C 0.494505 0.740741
195 ZAS 0.494382 0.7375
196 NAE 0.491803 0.860759
197 7MD 0.490909 0.831325
198 NA7 0.490385 0.921053
199 AVV 0.490196 0.935065
200 V3L 0.489796 0.932432
201 2AM 0.488636 0.905405
202 NAQ 0.487805 0.839506
203 P5A 0.485714 0.72043
204 LSS 0.485437 0.736264
205 VMS 0.485149 0.761364
206 NO7 0.485149 0.896104
207 54H 0.485149 0.761364
208 ZID 0.483871 0.883117
209 M24 0.483607 0.8875
210 DSH 0.483516 0.698795
211 9K8 0.481132 0.747253
212 8X1 0.480392 0.728261
213 5CA 0.480392 0.772727
214 AV2 0.48 0.881579
215 SFG 0.479167 0.721519
216 CUU 0.479167 0.932432
217 NAD TDB 0.478261 0.881579
218 NAD IBO 0.478261 0.881579
219 A3N 0.478261 0.75641
220 IMO 0.478261 0.891892
221 LPA AMP 0.477876 0.788235
222 EAD 0.47619 0.841463
223 DZD 0.475 0.851852
224 3AT 0.474747 0.932432
225 GJV 0.473118 0.722892
226 S4M 0.473118 0.644444
227 6MZ 0.473118 0.893333
228 OVE 0.472527 0.87013
229 38V 0.472 0.853659
230 KAA 0.471698 0.728261
231 YLY 0.471545 0.781609
232 NSS 0.471154 0.772727
233 DSZ 0.471154 0.772727
234 FDA 0.469697 0.804598
235 A5D 0.469388 0.75641
236 MAO 0.468085 0.732558
237 D4F 0.467742 0.809524
238 4TA 0.466667 0.77907
239 NVA LMS 0.466667 0.728261
240 NDC 0.465649 0.839506
241 7MC 0.465517 0.811765
242 O02 0.464646 0.886076
243 DAT 0.463918 0.87013
244 5X8 0.463918 0.734177
245 A6D 0.462264 0.697674
246 LEU LMS 0.462264 0.706522
247 P1H 0.461538 0.821429
248 NDE 0.461538 0.896104
249 N0B 0.460317 0.790698
250 DTP 0.46 0.87013
251 NWW 0.458824 0.72973
252 GSU 0.457944 0.752809
253 NAJ PZO 0.455285 0.817073
254 6FA 0.455224 0.811765
255 FB0 0.454545 0.777778
256 AMP NAD 0.454545 0.87013
257 71V 0.452632 0.873418
258 A3G 0.451613 0.769231
259 5AD 0.451219 0.716216
260 B1U 0.45045 0.712766
261 LQJ 0.45045 0.881579
262 YSA 0.45045 0.752809
263 6C6 0.45 0.848101
264 FAS 0.448529 0.821429
265 SFD 0.448529 0.71134
266 FAD 0.448529 0.821429
267 Y3J 0.447059 0.767123
268 ODP 0.446281 0.875
269 NJP 0.446281 0.909091
270 J4G 0.444444 0.884615
271 A3S 0.443299 0.779221
272 A7D 0.443299 0.746835
273 7DD 0.443299 0.945205
274 0WD 0.442623 0.886076
275 7C5 0.442478 0.7875
276 NPW 0.441667 0.853659
277 8PZ 0.441441 0.772727
278 RGT 0.441441 0.921053
279 K3K 0.441441 0.772152
280 NAJ PYZ 0.440945 0.821429
281 SA8 0.44 0.682353
282 MHZ 0.438776 0.674157
283 GGZ 0.438095 0.795181
284 9JJ 0.4375 0.9
285 FNK 0.435714 0.777778
286 62F 0.435714 0.831325
287 SAH 0.435644 0.716049
288 SAI 0.435644 0.707317
289 PO4 PO4 A A A A PO4 0.435185 0.866667
290 Z5A 0.434109 0.752809
291 K3E 0.433628 0.7625
292 SMM 0.432692 0.662921
293 V47 0.432692 0.753247
294 FAY 0.432624 0.831325
295 SAM 0.431373 0.666667
296 6IA 0.431373 0.807229
297 DDS 0.431373 0.844156
298 7DT 0.43 0.945205
299 0UM 0.429907 0.674419
300 NDP 0.429752 0.886076
301 RFL 0.429577 0.793103
302 7D7 0.428571 0.714286
303 ETB 0.428571 0.804598
304 DCA 0.428571 0.795455
305 KOY 0.42735 0.772152
306 AAT 0.427184 0.682353
307 EEM 0.427184 0.666667
308 TXP 0.42623 0.886076
309 NZQ 0.42623 0.875
310 N6P 0.425926 0.878378
311 PUA 0.425197 0.851852
312 APU 0.425 0.860759
313 PGS 0.424242 0.85
314 128 0.423729 0.75
315 2SA 0.423077 0.896104
316 30N 0.423077 0.729167
317 4YB 0.422414 0.736264
318 0T1 0.421875 0.795455
319 COA 0.421875 0.795455
320 P5F 0.421769 0.795455
321 GP3 0.421569 0.886076
322 NEC 0.421053 0.717949
323 DA 0.421053 0.844156
324 D5M 0.421053 0.844156
325 QXP 0.420561 0.758621
326 6K6 0.420561 0.893333
327 WSA 0.420168 0.761364
328 649 0.420168 0.72043
329 NIA 0.419355 0.792683
330 S7M 0.419048 0.666667
331 12D 0.418803 0.758621
332 GDP 0.417476 0.884615
333 FCX 0.416667 0.829545
334 FAM 0.416667 0.83908
335 AAM 0.416667 0.931507
336 F2N 0.416107 0.786517
337 GCP 0.415094 0.8625
338 O05 0.414414 0.813953
339 GNH 0.413462 0.873418
340 FA9 0.413333 0.833333
341 C2R 0.413043 0.868421
342 AMZ 0.413043 0.88
343 K2H 0.412844 0.728395
344 COS 0.412214 0.777778
345 CAO 0.412214 0.769231
346 AMX 0.412214 0.804598
347 9BG 0.41129 0.8625
348 KGA 0.410072 0.721649
349 SCO 0.409091 0.795455
350 QXG 0.409091 0.75
351 CMX 0.409091 0.795455
352 V1N 0.408696 0.881579
353 NWQ 0.408602 0.710526
354 XNP 0.408 0.841463
355 FAJ 0.407895 0.802326
356 YZS 0.407407 0.707071
357 KGP 0.407407 0.707071
358 MCD 0.407407 0.777778
359 GEK 0.407407 0.710843
360 N5O 0.40625 0.734177
361 ACO 0.406015 0.769231
362 A3T 0.405941 0.789474
363 GTP 0.40566 0.884615
364 K2K 0.405405 0.710843
365 R2V 0.405405 0.758621
366 8Q2 0.404959 0.747253
367 NAP 0.40458 0.907895
368 AIR 0.404494 0.864865
369 NMX 0.404412 0.736842
370 HAX 0.402985 0.777778
371 G1R 0.401869 0.873418
372 ANZ 0.401709 0.8375
373 TAP 0.401515 0.873418
374 J7V 0.401515 0.804598
375 2MC 0.40146 0.744681
376 62X 0.4 0.644444
377 GDD 0.4 0.851852
378 DZ4 0.4 0.848101
379 GKE 0.4 0.851852
380 COF 0.4 0.820225
381 GDC 0.4 0.851852
382 FYN 0.4 0.795455
383 K2W 0.4 0.714286
384 QBQ 0.4 0.871795
385 3KK 0.4 0.777778
Similar Ligands (3D)
Ligand no: 1; Ligand: ATF; Similar ligands found: 11
No: Ligand Similarity coefficient
1 GNP 0.9160
2 BEF GDP 0.9089
3 GSP 0.9078
4 ALF GDP 0.9014
5 GDP BEF 0.9008
6 GDP ALF 0.8998
7 GDP AF3 0.8968
8 DBG 0.8897
9 ADP ALF 0.8877
10 9GM 0.8804
11 UTP 0.8669
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1AKY; Ligand: AP5; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 1aky.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 2AWN ADP 4.09091
2 2AWN ADP 4.09091
3 1LVG ADP 5.05051
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