Receptor
PDB id Resolution Class Description Source Keywords
6ZJB 1.82 Å EC: 2.7.4.10 CRYSTAL STRUCTURE OF HUMAN ADENYLATE KINASE 3, AK3, IN COMPL INHIBITOR GP5A HOMO SAPIENS GTP:AMP PHOSPHOTRANSFERASE GP5A TRANSFERASE
Ref.: STRUCTURAL BASIS FOR GTP VERSUS ATP SELECTIVITY IN KINASE AK3. BIOCHEMISTRY V. 59 3570 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G5P C:301;
A:301;
F:301;
B:301;
D:301;
E:301;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
 submit data
932.366 C20 H29 N10 O23 P5 c1nc(...
MG C:302;
A:302;
F:302;
B:302;
D:302;
E:302;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6ZJD 1.75 Å EC: 2.7.4.10 CRYSTAL STRUCTURE OF HUMAN ADENYLATE KINASE 3, AK3, IN COMPL INHIBITOR ATP HOMO SAPIENS GTP:AMP PHOSPHOTRANSFERASE GP5A TRANSFERASE
Ref.: STRUCTURAL BASIS FOR GTP VERSUS ATP SELECTIVITY IN KINASE AK3. BIOCHEMISTRY V. 59 3570 2020
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6ZJE - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
2 2AK3 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 6ZJB - G5P C20 H29 N10 O23 P5 c1nc(c2c(n....
4 6ZJD Kd = 13 uM ATP C10 H16 N5 O13 P3 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 1 families.
1 6ZJE - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
2 2AK3 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 6ZJB - G5P C20 H29 N10 O23 P5 c1nc(c2c(n....
4 6ZJD Kd = 13 uM ATP C10 H16 N5 O13 P3 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: G5P; Similar ligands found: 372
No: Ligand ECFP6 Tc MDL keys Tc
1 G5P 1 1
2 G3A 0.988889 1
3 GP3 0.788889 1
4 GTP 0.755319 0.973684
5 GDP 0.723404 0.973684
6 AP5 0.722222 0.921053
7 B4P 0.722222 0.921053
8 GSP 0.721649 0.925
9 BA3 0.711111 0.921053
10 GNH 0.697917 0.961039
11 G1R 0.693878 0.961039
12 GCP 0.693878 0.948718
13 GTA 0.691589 0.962025
14 5FA 0.691489 0.921053
15 AQP 0.691489 0.921053
16 GNP 0.686869 0.948718
17 9GM 0.686869 0.948718
18 ATP 0.680851 0.921053
19 HEJ 0.680851 0.921053
20 A2D 0.67033 0.921053
21 G 0.670213 0.960526
22 5GP 0.670213 0.960526
23 GTG 0.663551 0.962025
24 GKE 0.654206 0.961538
25 GDD 0.654206 0.961538
26 GDC 0.654206 0.961538
27 G2R 0.653846 0.936709
28 GMV 0.65 0.948718
29 AGS 0.649485 0.875
30 ADP 0.648936 0.921053
31 AT4 0.642105 0.886076
32 GAV 0.640777 0.936709
33 G2P 0.637255 0.936709
34 ANP 0.636364 0.897436
35 GP2 0.636364 0.936709
36 A4P 0.626087 0.892857
37 AN2 0.625 0.909091
38 Y9Z 0.623853 0.880952
39 AR6 0.622449 0.896104
40 APR 0.622449 0.896104
41 ACQ 0.62 0.897436
42 M33 0.618557 0.884615
43 GFB 0.618182 0.961538
44 GDR 0.618182 0.961538
45 6YZ 0.617647 0.897436
46 GPG 0.616822 0.987013
47 AD9 0.616162 0.897436
48 GKD 0.616071 0.961538
49 UP5 0.614035 0.898734
50 6CK 0.612613 0.9375
51 ACP 0.612245 0.897436
52 CA0 0.602041 0.897436
53 ALF 5GP 0.601942 0.86747
54 JB2 0.60177 0.961538
55 YGP 0.6 0.902439
56 GPD 0.596491 0.925926
57 GDX 0.596491 0.974026
58 GDP BEF 0.596154 0.911392
59 KG4 0.59596 0.897436
60 A1R 0.59434 0.841463
61 ATF 0.592233 0.886076
62 GTP MG 0.590476 0.935065
63 CAG 0.590164 0.904762
64 T5A 0.588235 0.825581
65 ADX 0.585859 0.811765
66 A 0.585106 0.894737
67 AMP 0.585106 0.894737
68 JB3 0.584746 0.949367
69 APC G U 0.584 0.911392
70 GDP AF3 0.583333 0.86747
71 25L 0.581818 0.934211
72 HQG 0.580952 0.909091
73 50T 0.58 0.884615
74 ADQ 0.579439 0.897436
75 A3R 0.579439 0.841463
76 A22 0.575472 0.934211
77 TPG 0.574803 0.842697
78 PRX 0.574257 0.82716
79 TAT 0.572816 0.886076
80 T99 0.572816 0.886076
81 0O2 0.572727 0.960526
82 GDP ALF 0.568807 0.86747
83 8LE 0.567308 0.851852
84 5AL 0.567308 0.884615
85 45A 0.56701 0.848101
86 ABM 0.56701 0.848101
87 NGD 0.566667 0.987013
88 2MD 0.565574 0.892857
89 4AD 0.564815 0.875
90 AMP MG 0.5625 0.857143
91 JNT 0.559633 0.873418
92 APC 0.558824 0.886076
93 8LH 0.556604 0.8625
94 SRP 0.556604 0.8625
95 AP2 0.555556 0.886076
96 8QN 0.555556 0.884615
97 A12 0.555556 0.886076
98 OAD 0.554545 0.897436
99 9X8 0.554545 0.851852
100 GMP 0.553191 0.857143
101 MGD 0.552 0.892857
102 4TC 0.55 0.876543
103 BEF ADP 0.548077 0.848101
104 SRA 0.546392 0.85
105 G3D 0.546296 0.960526
106 MAP 0.546296 0.875
107 8LQ 0.546296 0.8625
108 QA7 0.546296 0.851852
109 00A 0.545455 0.864198
110 3OD 0.544643 0.897436
111 BIS 0.544643 0.864198
112 ADP MG 0.544554 0.87013
113 ADP BEF 0.544554 0.87013
114 5SV 0.541284 0.788235
115 OOB 0.541284 0.909091
116 U2G 0.540984 0.9375
117 FEG 0.540984 0.903614
118 AU1 0.539216 0.897436
119 APC MG 0.538462 0.848101
120 ZGP 0.536585 0.892857
121 139 0.536585 0.855422
122 AMO 0.536364 0.886076
123 PAJ 0.536364 0.843373
124 G4P 0.536364 0.960526
125 PR8 0.535714 0.811765
126 LAD 0.535714 0.821429
127 WAQ 0.535714 0.841463
128 1YD 0.534483 0.947368
129 4BW 0.534483 0.947368
130 VO4 ADP 0.53271 0.873418
131 CG2 0.532258 0.9375
132 DLL 0.531532 0.909091
133 1ZZ 0.530973 0.802326
134 KMQ 0.530435 0.8625
135 GH3 0.527273 0.948052
136 25A 0.527273 0.921053
137 OZV 0.527273 0.896104
138 3UK 0.526786 0.922078
139 GDP 7MG 0.525424 0.936709
140 UPA 0.52459 0.8875
141 7D4 0.524272 0.8375
142 ADP PO3 0.52381 0.87013
143 ADV 0.52381 0.8625
144 RBY 0.52381 0.8625
145 ATP MG 0.52381 0.87013
146 KB7 0.523364 0.807229
147 M7G A2M G 0.523179 0.831461
148 MD1 0.523077 0.892857
149 PGD 0.523077 0.925926
150 B5V 0.522124 0.910256
151 9SN 0.521739 0.876543
152 4UV 0.521368 0.875
153 DND 0.520661 0.910256
154 AHX 0.517857 0.853659
155 TXA 0.517544 0.886076
156 ME8 0.517544 0.802326
157 PTJ 0.517544 0.853659
158 NB8 0.517544 0.853659
159 B5Y 0.517241 0.898734
160 TXE 0.516393 0.8875
161 FE9 0.515385 0.778947
162 AFH 0.512605 0.843373
163 4UU 0.512605 0.875
164 ITT 0.509615 0.87013
165 V2G 0.509259 0.853659
166 QBQ 0.509259 0.960526
167 DGT 0.509091 0.9
168 DQV 0.508333 0.934211
169 TXD 0.508197 0.8875
170 4UW 0.508197 0.843373
171 3GP 0.504854 0.922078
172 ALF ADP 0.504587 0.807229
173 ANP MG 0.504587 0.860759
174 FYA 0.504348 0.860759
175 B5M 0.504274 0.898734
176 FA5 0.504274 0.886076
177 OMR 0.504065 0.813953
178 G1R G1R 0.503759 0.949367
179 38V 0.503759 0.962025
180 DBG 0.503759 0.974359
181 GAP 0.5 0.85
182 YLP 0.5 0.784091
183 48N 0.5 0.9
184 SON 0.5 0.886076
185 G4M 0.5 0.904762
186 NAI 0.495935 0.8875
187 NAX 0.495935 0.855422
188 6V0 0.495935 0.876543
189 JBT 0.494186 0.8
190 F2R 0.492188 0.891566
191 KBD 0.491379 0.851852
192 DAL AMP 0.491071 0.860759
193 JSQ 0.490741 0.875
194 HFD 0.490741 0.875
195 LMS 0.49 0.770115
196 ADJ 0.488189 0.813953
197 L3W 0.488 0.886076
198 YLC 0.488 0.802326
199 YLB 0.488 0.784091
200 AP0 0.488 0.853659
201 XAH 0.487395 0.802326
202 9ZA 0.486726 0.864198
203 9ZD 0.486726 0.864198
204 6G0 0.486486 0.936709
205 2A5 0.485981 0.85
206 7D3 0.485437 0.8375
207 G1G 0.484848 0.95
208 CNA 0.484375 0.910256
209 4UR 0.484127 0.947368
210 PAP 0.481481 0.907895
211 ATR 0.481481 0.894737
212 I2C FE2 CMO CMO 0.481203 0.811111
213 TYM 0.48 0.886076
214 LAQ 0.479675 0.802326
215 1YC 0.479339 0.921053
216 GPX 0.478261 0.922078
217 MGP 0.477477 0.936709
218 NAD 0.476923 0.909091
219 YLA 0.476562 0.784091
220 2GP 0.47619 0.935065
221 GA7 0.47541 0.8625
222 KBJ 0.475 0.821429
223 ADP BMA 0.474138 0.873418
224 AYB 0.472868 0.775281
225 3AT 0.472727 0.896104
226 DGI 0.472727 0.9
227 A3D 0.469697 0.897436
228 A2R 0.469027 0.909091
229 IOT 0.46875 0.858824
230 IDP 0.46789 0.947368
231 JB6 0.466102 0.841463
232 AOC 0.466019 0.759494
233 COD 0.465649 0.777778
234 5AS 0.462264 0.728261
235 MYR AMP 0.462185 0.781609
236 BT5 0.462121 0.795455
237 CZF 0.459459 0.909091
238 YLY 0.459259 0.775281
239 80F 0.458647 0.825581
240 FDA 0.458333 0.83908
241 RAB 0.457447 0.779221
242 XYA 0.457447 0.779221
243 ADN 0.457447 0.779221
244 BGO 0.457364 0.949367
245 AKW 0.457364 0.914634
246 PGD O 0.456522 0.852273
247 D4F 0.455882 0.86747
248 7C5 0.455285 0.896104
249 6FA 0.455172 0.891566
250 ATP A 0.454545 0.883117
251 ATP A A A 0.454545 0.883117
252 BTX 0.454545 0.804598
253 4TA 0.454545 0.793103
254 EAD 0.453237 0.855422
255 AR6 AR6 0.451613 0.871795
256 ARG AMP 0.451613 0.857143
257 R7I 0.451327 0.922078
258 R5I 0.451327 0.922078
259 ZID 0.449275 0.922078
260 N0B 0.449275 0.804598
261 FAD 0.44898 0.902439
262 FAS 0.44898 0.902439
263 M24 0.448529 0.855422
264 5N5 0.447917 0.75641
265 GGM 0.44697 0.925926
266 DTP 0.446429 0.8375
267 7D5 0.445545 0.8125
268 P1G 0.445455 0.85
269 NAE 0.445255 0.898734
270 EP4 0.444444 0.698795
271 AHZ 0.444444 0.802326
272 FAY 0.443709 0.91358
273 A4D 0.443299 0.75641
274 5CD 0.443299 0.74359
275 6AD 0.442478 0.843373
276 NAQ 0.442029 0.876543
277 NAD IBO 0.44186 0.896104
278 NAD TDB 0.44186 0.896104
279 ARU 0.440678 0.8
280 P1H 0.440559 0.835294
281 P2G 0.440367 0.860759
282 7MD 0.44 0.823529
283 TSB 0.439655 0.784091
284 8X1 0.439655 0.723404
285 A3P 0.439252 0.894737
286 SFD 0.439189 0.778947
287 G5A 0.4375 0.747253
288 NA7 0.436975 0.886076
289 3AM 0.436893 0.857143
290 TAD 0.436508 0.843373
291 H1Q 0.436364 0.835443
292 CUU 0.436364 0.896104
293 AMP DBH 0.435484 0.873418
294 SSA 0.434783 0.766667
295 AF3 ADP 3PG 0.434109 0.8
296 DDS 0.433628 0.8125
297 P5A 0.433333 0.715789
298 AMP NAD 0.432836 0.884615
299 RFL 0.431373 0.870588
300 DGP 0.431193 0.8875
301 DG 0.431193 0.8875
302 VMS 0.431034 0.755556
303 NO7 0.431034 0.8625
304 54H 0.431034 0.755556
305 PPS 0.429825 0.811765
306 FNK 0.427632 0.811111
307 3DH 0.427184 0.716049
308 GPC 0.426471 0.880952
309 128 0.426357 0.784091
310 A5A 0.426087 0.772727
311 AV2 0.426087 0.848101
312 MAO 0.425926 0.707865
313 A2P 0.425926 0.881579
314 M2T 0.425743 0.682353
315 DTA 0.425743 0.75
316 Z5A 0.425532 0.786517
317 ODP 0.425373 0.936709
318 G C 0.425373 0.901235
319 9BG 0.425373 0.974026
320 FB0 0.424658 0.771739
321 NDC 0.424658 0.876543
322 AVV 0.423729 0.831325
323 NAJ PZO 0.423358 0.831325
324 ALF ADP 3PG 0.423077 0.8
325 IMP 0.422018 0.934211
326 MTA 0.421569 0.716049
327 V3L 0.421053 0.896104
328 NDE 0.42069 0.935065
329 NSS 0.420168 0.766667
330 7MC 0.419847 0.804598
331 7DT 0.419643 0.907895
332 RGT 0.419355 0.910256
333 DZD 0.419118 0.865854
334 52H 0.418803 0.747253
335 LPA AMP 0.418605 0.781609
336 9K8 0.418033 0.723404
337 PUA 0.417266 0.865854
338 NVA LMS 0.416667 0.723404
339 APU 0.416667 0.875
340 5CA 0.415254 0.766667
341 53H 0.415254 0.747253
342 6RE 0.415094 0.768293
343 P5F 0.415094 0.872093
344 NJP 0.414815 0.923077
345 G2Q 0.413223 0.936709
346 LEU LMS 0.413223 0.72043
347 O02 0.412281 0.876543
348 DAT 0.410714 0.8375
349 LSS 0.408333 0.731183
350 DSZ 0.408333 0.766667
351 01G 0.408 0.903614
352 IMO 0.407407 0.857143
353 J7C 0.407407 0.777778
354 A3N 0.407407 0.728395
355 ZAS 0.40566 0.731707
356 G7M 0.405405 0.924051
357 LQJ 0.404762 0.871795
358 S4M 0.40367 0.623656
359 GJV 0.40367 0.759036
360 6MZ 0.40367 0.858974
361 SA8 0.403509 0.678161
362 OVE 0.401869 0.8375
363 MHZ 0.401786 0.652174
364 SGP 0.401786 0.807229
365 0WD 0.40146 0.9
366 NAJ PYZ 0.401408 0.793103
367 F2N 0.401235 0.820225
368 35G 0.4 0.934211
369 2AM 0.4 0.87013
370 J1A 0.4 0.75
371 C2E 0.4 0.947368
372 PCG 0.4 0.934211
Similar Ligands (3D)
Ligand no: 1; Ligand: G5P; Similar ligands found: 1
No: Ligand Similarity coefficient
1 UDP ADP BF2 0.8760
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6ZJD; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6zjd.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
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