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- ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP SACCHAROMYCES CEREVISIAE NUCLEOSIDE MONOPHOSPHATE KINASE MYOKINASE TRANSFERASE (PHOSPHOTRANSFERASE)
Ref.: STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN 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;
submit data
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 16 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 9 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 (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 1E4V - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
11 4X8L - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
12 1AKE - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
13 3HPQ - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
14 1ANK - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
15 4X8O Kd = 60 nM AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
16 5G40 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
17 5G3Z - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
18 5G41 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
19 2RGX - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
20 4UKD - UDP ADP BF2 n/a n/a
21 1QF9 - ALF Al F4 F[Al-](F)(....
22 2UKD - C5P C9 H14 N3 O8 P C1=CN(C(=O....
23 1S3G - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
24 3FB4 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
25 4MKG - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
26 4MKH - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
27 5G3Y - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
28 1UKY - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1UKZ - AMP C10 H14 N5 O7 P c1nc(c2c(n....
30 2BWJ - AMP C10 H14 N5 O7 P c1nc(c2c(n....
31 1ZIP - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
32 1ZIO - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
33 1ZIN - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
34 1Z83 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
35 4W5J - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
36 4NU0 - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
37 2CDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 2AK3 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ATF; Similar ligands found: 329
No: Ligand ECFP6 Tc MDL keys Tc
1 ATF 1 1
2 A2D 0.789474 0.932432
3 BA3 0.769231 0.932432
4 AP5 0.759494 0.932432
5 ADP 0.759494 0.958904
6 B4P 0.759494 0.932432
7 AN2 0.75 0.945946
8 BIS 0.744444 0.973333
9 M33 0.740741 0.92
10 ATP 0.731707 0.958904
11 ACP 0.731707 0.933333
12 APR 0.722892 0.932432
13 5FA 0.722892 0.958904
14 AQP 0.722892 0.958904
15 AR6 0.722892 0.932432
16 ANP 0.717647 0.933333
17 AGS 0.714286 0.909091
18 SAP 0.714286 0.909091
19 AD9 0.714286 0.933333
20 A 0.705128 0.931507
21 AMP 0.705128 0.931507
22 CA0 0.698795 0.907895
23 ADX 0.698795 0.841463
24 ACQ 0.697674 0.933333
25 50T 0.690476 0.92
26 PRX 0.682353 0.858974
27 ABM 0.679012 0.881579
28 AMP MG 0.666667 0.857143
29 ADQ 0.663043 0.907895
30 A12 0.662651 0.921053
31 AP2 0.662651 0.921053
32 A22 0.659341 0.945946
33 SRA 0.654321 0.883117
34 5AL 0.651685 0.894737
35 A1R 0.645161 0.873418
36 APC 0.643678 0.921053
37 TAT 0.640449 0.921053
38 AU1 0.639535 0.933333
39 ADP MG 0.639535 0.87013
40 SRP 0.637363 0.871795
41 5SV 0.634409 0.817073
42 ADP BEF 0.632184 0.896104
43 BEF ADP 0.632184 0.896104
44 OAD 0.631579 0.907895
45 PAJ 0.62766 0.851852
46 AHX 0.621053 0.8625
47 00A 0.621053 0.897436
48 3OD 0.618557 0.907895
49 ADP PO3 0.617977 0.905405
50 ADV 0.617977 0.896104
51 RBY 0.617977 0.896104
52 OOB 0.617021 0.894737
53 8QN 0.617021 0.894737
54 25A 0.617021 0.932432
55 25L 0.612245 0.945946
56 ATP MG 0.611111 0.87013
57 4AD 0.610526 0.884615
58 AMO 0.610526 0.896104
59 ADP ALF 0.608696 0.909091
60 ALF ADP 0.608696 0.909091
61 PR8 0.608247 0.819277
62 LAD 0.608247 0.829268
63 MAP 0.606383 0.909091
64 9SN 0.606061 0.910256
65 DLL 0.604167 0.894737
66 PTJ 0.602041 0.8625
67 1ZZ 0.602041 0.809524
68 G3A 0.598039 0.886076
69 3UK 0.597938 0.883117
70 AFH 0.592233 0.923077
71 G5P 0.592233 0.886076
72 WAQ 0.591837 0.85
73 SON 0.590909 0.896104
74 GAP 0.586957 0.858974
75 GTA 0.586538 0.853659
76 TXA 0.585859 0.896104
77 NB8 0.585859 0.8625
78 ME8 0.585859 0.809524
79 FYA 0.585859 0.87013
80 ANP MG 0.585106 0.860759
81 VO4 ADP 0.585106 0.894737
82 ADP VO4 0.585106 0.894737
83 UP5 0.584906 0.884615
84 XAH 0.578431 0.809524
85 4TC 0.574074 0.8625
86 4UV 0.572816 0.860759
87 NAX 0.570093 0.841463
88 6V0 0.570093 0.8625
89 FA5 0.568627 0.871795
90 YAP 0.568627 0.860759
91 ADP BMA 0.565657 0.883117
92 OMR 0.564815 0.821429
93 4UU 0.561905 0.860759
94 48N 0.560748 0.8625
95 AP0 0.559633 0.8625
96 139 0.558559 0.841463
97 DAL AMP 0.556701 0.87013
98 DND 0.555556 0.896104
99 NXX 0.555556 0.896104
100 NAI 0.555556 0.873418
101 ARU 0.555556 0.875
102 TXD 0.555556 0.873418
103 A4P 0.554545 0.813953
104 2A5 0.554348 0.883117
105 AOC 0.551724 0.789474
106 XYA 0.551282 0.810811
107 ADN 0.551282 0.810811
108 RAB 0.551282 0.810811
109 TXE 0.550459 0.873418
110 ATR 0.548387 0.931507
111 PAP 0.548387 0.945205
112 UPA 0.545455 0.873418
113 T5A 0.544643 0.811765
114 5AS 0.544444 0.752809
115 COD 0.54386 0.784091
116 4UW 0.541284 0.829268
117 7D3 0.539326 0.87013
118 JB6 0.539216 0.85
119 5N5 0.5375 0.786667
120 LAQ 0.537037 0.809524
121 MYR AMP 0.533981 0.788235
122 7D4 0.532609 0.87013
123 ITT 0.532609 0.905405
124 YLP 0.53211 0.790698
125 ADJ 0.530973 0.821429
126 A4D 0.530864 0.786667
127 5CD 0.530864 0.797297
128 A2R 0.530612 0.945946
129 A A 0.529412 0.906667
130 CNA 0.526316 0.896104
131 ATP A A A 0.52381 0.893333
132 6RE 0.522727 0.731707
133 TYM 0.522523 0.871795
134 IOT 0.522124 0.802326
135 AR6 AR6 0.518519 0.881579
136 YLC 0.517857 0.809524
137 YLB 0.517857 0.790698
138 NAD 0.517241 0.894737
139 3AM 0.517241 0.891892
140 BTX 0.517241 0.811765
141 A3P 0.516484 0.931507
142 BT5 0.512821 0.802326
143 EP4 0.511905 0.725
144 7D5 0.511628 0.844156
145 G5A 0.510417 0.752809
146 A3D 0.508475 0.883117
147 M2T 0.505882 0.707317
148 DTA 0.505882 0.75641
149 3DH 0.505747 0.74359
150 SSA 0.50505 0.772727
151 TYR AMP 0.504673 0.848101
152 YLA 0.504348 0.790698
153 6AD 0.5 0.875
154 AYB 0.5 0.781609
155 PPS 0.5 0.841463
156 A2P 0.5 0.917808
157 TAD 0.5 0.851852
158 52H 0.5 0.752809
159 MTA 0.5 0.74359
160 AMP DBH 0.5 0.858974
161 AF3 ADP 3PG 0.495575 0.875
162 ALF ADP 3PG 0.495575 0.875
163 LA8 ALF 3PG 0.495575 0.875
164 AHZ 0.495495 0.788235
165 ARG AMP 0.495495 0.8
166 TSB 0.49505 0.790698
167 53H 0.49505 0.752809
168 A5A 0.494949 0.77907
169 J7C 0.494505 0.740741
170 ZAS 0.494382 0.7375
171 NAE 0.491803 0.860759
172 7MD 0.490909 0.831325
173 NA7 0.490385 0.921053
174 AVV 0.490196 0.935065
175 V3L 0.489796 0.932432
176 2AM 0.488636 0.905405
177 NAQ 0.487805 0.839506
178 P5A 0.485714 0.72043
179 LSS 0.485437 0.736264
180 54H 0.485149 0.761364
181 VMS 0.485149 0.761364
182 ZID 0.483871 0.883117
183 M24 0.483607 0.8875
184 DSH 0.483516 0.698795
185 5CA 0.480392 0.772727
186 AV2 0.48 0.881579
187 SFG 0.479167 0.721519
188 IMO 0.478261 0.891892
189 A3N 0.478261 0.75641
190 LPA AMP 0.477876 0.788235
191 EAD 0.47619 0.841463
192 DZD 0.475 0.851852
193 3AT 0.474747 0.932432
194 S4M 0.473118 0.644444
195 GJV 0.473118 0.722892
196 OVE 0.472527 0.87013
197 KAA 0.471698 0.728261
198 YLY 0.471545 0.781609
199 NSS 0.471154 0.772727
200 DSZ 0.471154 0.772727
201 FDA 0.469697 0.804598
202 A5D 0.469388 0.75641
203 MAO 0.468085 0.732558
204 NVA LMS 0.466667 0.736264
205 4TA 0.466667 0.77907
206 NDC 0.465649 0.839506
207 7MC 0.465517 0.811765
208 DAT 0.463918 0.87013
209 5X8 0.463918 0.734177
210 A6D 0.462264 0.697674
211 LEU LMS 0.462264 0.736264
212 P1H 0.461538 0.821429
213 NDE 0.461538 0.896104
214 N0B 0.460317 0.790698
215 DTP 0.46 0.87013
216 NAD IBO 0.458333 0.8375
217 GSU 0.457944 0.752809
218 NAJ PZO 0.455285 0.817073
219 6FA 0.455224 0.811765
220 G A A A 0.454545 0.839506
221 FB0 0.454545 0.777778
222 71V 0.452632 0.873418
223 A3G 0.451613 0.769231
224 5AD 0.451219 0.716216
225 YSA 0.45045 0.752809
226 6C6 0.45 0.848101
227 SFD 0.448529 0.71134
228 FAD 0.448529 0.821429
229 FAS 0.448529 0.821429
230 Y3J 0.447059 0.767123
231 NJP 0.446281 0.909091
232 ODP 0.446281 0.875
233 7DD 0.443299 0.945205
234 A7D 0.443299 0.746835
235 A3S 0.443299 0.779221
236 0WD 0.442623 0.886076
237 7C5 0.442478 0.7875
238 NPW 0.441667 0.853659
239 RGT 0.441441 0.921053
240 NAJ PYZ 0.440945 0.864198
241 SA8 0.44 0.682353
242 U A G G 0.439024 0.85
243 MHZ 0.438776 0.674157
244 GGZ 0.438095 0.795181
245 FNK 0.435714 0.777778
246 62F 0.435714 0.831325
247 SAH 0.435644 0.716049
248 SAI 0.435644 0.707317
249 PO4 PO4 A A A A PO4 0.435185 0.866667
250 Z5A 0.434109 0.752809
251 SMM 0.432692 0.662921
252 FAY 0.432624 0.831325
253 SAM 0.431373 0.666667
254 DDS 0.431373 0.844156
255 6IA 0.431373 0.807229
256 7DT 0.43 0.945205
257 0UM 0.429907 0.674419
258 NDP 0.429752 0.886076
259 RFL 0.429577 0.793103
260 DCA 0.428571 0.795455
261 7D7 0.428571 0.714286
262 ETB 0.428571 0.804598
263 EEM 0.427184 0.666667
264 AAT 0.427184 0.682353
265 AMP NAD 0.426357 0.848101
266 TXP 0.42623 0.886076
267 NZQ 0.42623 0.875
268 N6P 0.425926 0.878378
269 PUA 0.425197 0.851852
270 A U 0.425 0.8375
271 APU 0.425 0.860759
272 PGS 0.424242 0.85
273 128 0.423729 0.75
274 2SA 0.423077 0.896104
275 30N 0.423077 0.729167
276 4YB 0.422414 0.736264
277 A A A 0.422018 0.87013
278 0T1 0.421875 0.795455
279 COA 0.421875 0.795455
280 P5F 0.421769 0.795455
281 GP3 0.421569 0.886076
282 D5M 0.421053 0.844156
283 DA 0.421053 0.844156
284 NEC 0.421053 0.717949
285 6K6 0.420561 0.893333
286 649 0.420168 0.72043
287 WSA 0.420168 0.761364
288 NIA 0.419355 0.792683
289 S7M 0.419048 0.666667
290 12D 0.418803 0.758621
291 GDP 0.417476 0.884615
292 FCX 0.416667 0.829545
293 FAM 0.416667 0.83908
294 AAM 0.416667 0.931507
295 F2N 0.416107 0.786517
296 GCP 0.415094 0.8625
297 GNH 0.413462 0.873418
298 FA9 0.413333 0.833333
299 C2R 0.413043 0.868421
300 AMZ 0.413043 0.88
301 COS 0.412214 0.777778
302 CAO 0.412214 0.769231
303 AMX 0.412214 0.804598
304 SCO 0.409091 0.795455
305 CMX 0.409091 0.795455
306 V1N 0.408696 0.881579
307 XNP 0.408 0.841463
308 GEK 0.407407 0.710843
309 MCD 0.407407 0.777778
310 ACO 0.406015 0.769231
311 A3T 0.405941 0.789474
312 GTP 0.40566 0.884615
313 NAP 0.40458 0.907895
314 AIR 0.404494 0.864865
315 NMX 0.404412 0.736842
316 HAX 0.402985 0.777778
317 G1R 0.401869 0.873418
318 ANZ 0.401709 0.8375
319 J7V 0.401515 0.804598
320 TAP 0.401515 0.873418
321 2MC 0.40146 0.744681
322 GDC 0.4 0.851852
323 GKE 0.4 0.851852
324 FYN 0.4 0.795455
325 3KK 0.4 0.777778
326 U G A 0.4 0.809524
327 COF 0.4 0.820225
328 GDD 0.4 0.851852
329 62X 0.4 0.644444
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1AKY; Ligand: AP5; Similar sites found: 42
This union binding pocket(no: 1) in the query (biounit: 1aky.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DPY ADP 0.001853 0.48274 1.81818
2 2BIF SIN 0.0005159 0.42869 2.27273
3 2BIF ANP 0.0001933 0.42581 2.27273
4 1P72 ADP 0.0003441 0.41662 2.27273
5 1VHT BA3 0.000009603 0.40209 2.75229
6 1TQ4 GDP 0.00175 0.44689 3.18182
7 1KA1 A3P 0.02997 0.40246 3.18182
8 1M7G ADX 0.0003446 0.41077 3.79147
9 1M7G ADP 0.0004165 0.40151 3.79147
10 1E2K TMC 0.00008206 0.4536 4.54545
11 2C04 GCP 0.01248 0.41443 4.54545
12 1LVK MNT BEF 0.003864 0.40364 5
13 1LVG ADP 0.0000001038 0.4119 5.05051
14 5H56 TYD 0.0000003482 0.50133 5.12821
15 5H56 ADP 0.0000003482 0.50133 5.12821
16 2YOH WMJ 0.00003726 0.44958 6.19048
17 4BQS ADP 0.00006007 0.46183 6.25
18 4BQS K2Q 0.00006007 0.44938 6.25
19 2FNA ADP 0.0007013 0.46087 6.36364
20 1NN5 ANP 0.0000005937 0.50002 6.51163
21 1NN5 2DT 0.001207 0.43275 6.51163
22 1M7B GTP 0.005352 0.42487 6.52174
23 3N5C GDP 0.0001391 0.52968 6.79012
24 1UJ2 C5P 0.00002699 0.42793 7.72727
25 1G8S MET 0.03173 0.4131 7.72727
26 1UJ2 ADP 0.0001144 0.41105 7.72727
27 4BFW ZVW 0.002254 0.40248 8.63636
28 2OFW ADX 0.0002404 0.43576 8.65385
29 3QBT GNP 0.002266 0.42841 9.1954
30 2PEZ GGZ 0.0001896 0.42416 10.0559
31 2PEZ DAT 0.0001896 0.42416 10.0559
32 1KO8 6PG 0.00002219 0.40704 10.2857
33 3GJ8 GDP 0.0003907 0.50085 11.3636
34 4Q1A 2XZ 0.00139 0.46171 13.1818
35 4Q1A UDP 0.00139 0.46171 13.1818
36 1X6V ADP 0.0001082 0.42061 13.1818
37 4TMK T5A 0.0005899 0.41034 14.554
38 3LXR GDP 0.0009857 0.47567 14.5833
39 2QG6 NMN 0.0001258 0.41513 16.0804
40 3TMK T5A 0.000002122 0.47225 17.1296
41 1ZUI SKM 0.000106 0.4408 17.2619
42 1HE1 GDP 0.002481 0.44002 34.8148
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