Receptor
PDB id Resolution Class Description Source Keywords
13PK 2.5 Å EC: 2.7.2.3 TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI TRYPANOSOMA BRUCEI KINASE PHOSPHOGLYCERATE TERNARY COMPLEX GLYCOLYSIS TRANSFERASE
Ref.: SYNERGISTIC EFFECTS OF SUBSTRATE-INDUCED CONFORMATIONAL CHANGES IN PHOSPHOGLYCERATE KINASE ACTIVATION. NATURE V. 385 275 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PG A:423;
B:423;
Valid;
Valid;
none;
none;
submit data
186.057 C3 H7 O7 P C([C@...
ADP A:421;
B:421;
C:421;
D:421;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
427.201 C10 H15 N5 O10 P2 c1nc(...
MG A:422;
B:422;
C:422;
D:422;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PO4 A:701;
A:704;
C:624;
C:702;
C:703;
D:625;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
16PK 1.6 Å EC: 2.7.2.3 PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG TRYPANOSOMA BRUCEI KINASE PHOSPHOGLYCERATE TERNARY COMPLEX GLYCOLYSIS TRANSFERASE BISUBSTRATE ANALOG
Ref.: A BISUBSTRATE ANALOG INDUCES UNEXPECTED CONFORMATIONAL CHANGES IN PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI. J.MOL.BIOL. V. 279 1137 1998
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
4 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
5 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
6 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
7 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
9 2WZC - ALF ADP 3PG n/a n/a
10 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 2WZD - AF3 ADP 3PG n/a n/a
13 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
15 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
16 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
17 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
18 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
19 2YBE - LA8 ALF 3PG n/a n/a
20 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
21 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
22 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
23 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
26 3ZLB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
27 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PG; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 3PG 1 1
2 DEZ 0.575758 0.941176
3 DER 0.575758 0.941176
4 SEP 0.515152 0.74359
5 4TP 0.5 0.780488
6 R10 0.486486 0.941176
7 PA5 0.486486 0.941176
8 DG2 0.485714 0.909091
9 6PG 0.461538 0.941176
10 LG6 0.461538 0.941176
11 1GP 0.4375 0.852941
12 G3P 0.4375 0.852941
13 PGA 0.433333 0.90625
14 DXP 0.432432 0.911765
15 M2P 0.424242 0.857143
16 G3H 0.411765 0.9375
17 5SP 0.410256 0.837838
18 D5X 0.410256 0.941176
19 HMS 0.410256 0.837838
20 5RP 0.410256 0.837838
21 0V5 0.40625 0.727273
22 PEQ 0.40625 0.727273
23 RUB 0.4 0.885714
24 RES 0.4 0.659574
25 XBP 0.4 0.885714
Ligand no: 2; Ligand: ADP; Similar ligands found: 382
No: Ligand ECFP6 Tc MDL keys Tc
1 ADP 1 1
2 ATP 0.9 1
3 A2D 0.895522 0.971831
4 5FA 0.887324 1
5 AQP 0.887324 1
6 B4P 0.884058 0.971831
7 AP5 0.884058 0.971831
8 BA3 0.869565 0.971831
9 M33 0.833333 0.958333
10 ACQ 0.826667 0.972222
11 A 0.823529 0.971429
12 AMP 0.823529 0.971429
13 ACP 0.821918 0.972222
14 AR6 0.810811 0.971831
15 APR 0.810811 0.971831
16 ANP 0.802632 0.972222
17 AD9 0.8 0.972222
18 AGS 0.8 0.945946
19 SAP 0.8 0.945946
20 ADX 0.783784 0.873418
21 CA0 0.783784 0.945205
22 TAT 0.779221 0.958904
23 AMP MG 0.774648 0.891892
24 50T 0.773333 0.958333
25 ABM 0.763889 0.917808
26 PRX 0.763158 0.893333
27 APC 0.763158 0.958904
28 ATF 0.759494 0.958904
29 A22 0.753086 0.985915
30 AP2 0.743243 0.958904
31 A12 0.743243 0.958904
32 ADP MG 0.736842 0.905405
33 SRA 0.736111 0.918919
34 ADQ 0.73494 0.945205
35 25L 0.732558 0.985915
36 ADP BEF 0.727273 0.881579
37 BEF ADP 0.727273 0.881579
38 5AL 0.725 0.931507
39 2A5 0.717949 0.918919
40 A1R 0.714286 0.907895
41 AU1 0.714286 0.972222
42 ADP PO3 0.708861 0.943662
43 PAP 0.708861 0.985714
44 ATR 0.708861 0.971429
45 SRP 0.707317 0.906667
46 25A 0.702381 0.971831
47 ATP MG 0.7 0.905405
48 OAD 0.697674 0.945205
49 ADV 0.6875 0.932432
50 RBY 0.6875 0.932432
51 00A 0.686047 0.883117
52 BIS 0.681818 0.933333
53 3OD 0.681818 0.945205
54 ADP ALF 0.674699 0.87013
55 ALF ADP 0.674699 0.87013
56 AMO 0.674419 0.932432
57 4AD 0.674419 0.92
58 PAJ 0.674419 0.884615
59 GAP 0.670732 0.893333
60 MAP 0.670588 0.945946
61 ADP VO4 0.666667 0.931507
62 DLL 0.666667 0.931507
63 AHX 0.666667 0.896104
64 ANP MG 0.666667 0.894737
65 PTJ 0.662921 0.896104
66 SON 0.658228 0.932432
67 PR8 0.651685 0.85
68 LAD 0.651685 0.860759
69 ITT 0.65 0.943662
70 G5P 0.648936 0.921053
71 XYA 0.647059 0.84507
72 RAB 0.647059 0.84507
73 ADN 0.647059 0.84507
74 NB8 0.644444 0.896104
75 ME8 0.644444 0.839506
76 FYA 0.644444 0.905405
77 TXA 0.644444 0.932432
78 1ZZ 0.644444 0.839506
79 6AD 0.642857 0.909091
80 ADP BMA 0.640449 0.918919
81 G3A 0.638298 0.921053
82 DAL AMP 0.632184 0.905405
83 AFH 0.631579 0.884615
84 GTA 0.625 0.886076
85 FA5 0.623656 0.906667
86 YAP 0.623656 0.894737
87 UP5 0.622449 0.92
88 XAH 0.617021 0.839506
89 AV2 0.616279 0.917808
90 AOC 0.615385 0.821918
91 NAI 0.606061 0.907895
92 DND 0.606061 0.932432
93 TXD 0.606061 0.907895
94 NAX 0.606061 0.873418
95 NXX 0.606061 0.932432
96 5N5 0.605634 0.819444
97 5AS 0.604938 0.77907
98 A4P 0.60396 0.843373
99 DAT 0.60241 0.905405
100 A2R 0.602273 0.985915
101 5CD 0.597222 0.805556
102 A4D 0.597222 0.819444
103 4TC 0.594059 0.896104
104 AP0 0.594059 0.896104
105 A3P 0.592593 0.971429
106 139 0.592233 0.873418
107 T5A 0.592233 0.841463
108 ATP A A A 0.589474 0.930556
109 LAQ 0.585859 0.839506
110 MYR AMP 0.585106 0.817073
111 YLP 0.58 0.819277
112 UPA 0.578431 0.907895
113 ADJ 0.576923 0.851852
114 3AM 0.576923 0.929577
115 COD 0.575472 0.811765
116 NAD 0.575472 0.931507
117 3AT 0.574713 0.971831
118 EP4 0.573333 0.753247
119 A2P 0.573171 0.957143
120 CNA 0.571429 0.932432
121 TYM 0.568627 0.906667
122 PPS 0.568182 0.873418
123 M2T 0.565789 0.734177
124 DTA 0.565789 0.786667
125 AR6 AR6 0.565657 0.917808
126 A3D 0.564815 0.918919
127 3DH 0.564103 0.773333
128 G5A 0.563218 0.77907
129 YLB 0.563107 0.819277
130 YLC 0.563107 0.839506
131 AMP DBH 0.561224 0.893333
132 MTA 0.558442 0.773333
133 DTP 0.556818 0.905405
134 AHZ 0.554455 0.817073
135 NA7 0.553191 0.958904
136 IOT 0.552381 0.831325
137 ZAS 0.55 0.766234
138 7MD 0.55 0.8625
139 IMO 0.548781 0.929577
140 YLA 0.54717 0.819277
141 NAE 0.544643 0.894737
142 TAD 0.544554 0.884615
143 A5A 0.544444 0.807229
144 2AM 0.544304 0.943662
145 TSB 0.543478 0.819277
146 AYB 0.542056 0.809524
147 NAQ 0.539823 0.871795
148 V3L 0.539326 0.971831
149 AF3 ADP 3PG 0.538462 0.8375
150 ALF ADP 3PG 0.538462 0.8375
151 LA8 ALF 3PG 0.538462 0.8375
152 SSA 0.538462 0.8
153 ZID 0.535088 0.918919
154 LPA AMP 0.533981 0.817073
155 54H 0.532609 0.788235
156 52H 0.532609 0.77907
157 VMS 0.532609 0.788235
158 BTX 0.53211 0.841463
159 A3N 0.53012 0.786667
160 BT5 0.527273 0.831325
161 5CA 0.526882 0.8
162 53H 0.526882 0.77907
163 ARU 0.526316 0.860759
164 EAD 0.525862 0.873418
165 RGT 0.525253 0.958904
166 OVE 0.52439 0.905405
167 S4M 0.52381 0.666667
168 GDP 0.522222 0.92
169 DDS 0.522222 0.878378
170 AVV 0.521277 0.896104
171 NDE 0.521008 0.932432
172 7MC 0.518868 0.841463
173 DSH 0.518072 0.725
174 MAO 0.517647 0.759036
175 NSS 0.515789 0.8
176 DSZ 0.515789 0.8
177 LSS 0.515789 0.761364
178 P5A 0.515464 0.744444
179 DZD 0.513514 0.884615
180 NVA LMS 0.510417 0.761364
181 12D 0.509615 0.785714
182 NAD IBO 0.509091 0.87013
183 M24 0.508772 0.85
184 YLY 0.508772 0.809524
185 P1H 0.508333 0.851852
186 5AD 0.506849 0.746479
187 LEU LMS 0.505155 0.761364
188 4TA 0.504505 0.807229
189 G A A A 0.504505 0.871795
190 NAJ PZO 0.504425 0.848101
191 NDC 0.5 0.871795
192 128 0.5 0.776471
193 A3G 0.5 0.8
194 KAA 0.5 0.752809
195 GSU 0.5 0.77907
196 N0B 0.495726 0.819277
197 NJP 0.495495 0.945946
198 ODP 0.495495 0.909091
199 2SA 0.494624 0.932432
200 6C6 0.494505 0.881579
201 SFG 0.494382 0.75
202 0WD 0.491071 0.921053
203 YSA 0.490196 0.77907
204 PO4 PO4 A A A A PO4 0.489796 0.902778
205 SAM 0.48913 0.690476
206 6IA 0.48913 0.8375
207 A7D 0.488636 0.776316
208 6FA 0.488 0.841463
209 FB0 0.487805 0.804598
210 NAJ PYZ 0.487179 0.85
211 A5D 0.483516 0.786667
212 IDP 0.483516 0.918919
213 SA8 0.483516 0.707317
214 PGS 0.483146 0.883117
215 MHZ 0.483146 0.697674
216 NEC 0.482353 0.746667
217 D5M 0.482353 0.878378
218 DA 0.482353 0.878378
219 NIA 0.481928 0.822785
220 FAD 0.480315 0.851852
221 FAS 0.480315 0.851852
222 FDA 0.48 0.833333
223 N6P 0.479592 0.915493
224 GGZ 0.479167 0.825
225 SAI 0.478261 0.734177
226 SAH 0.478261 0.74359
227 NDP 0.477477 0.921053
228 NPW 0.477477 0.886076
229 AAM 0.476744 0.971429
230 C2R 0.47561 0.90411
231 AMZ 0.47561 0.916667
232 A A A 0.474747 0.905405
233 GTP 0.473684 0.92
234 SMM 0.473684 0.686047
235 TXP 0.473214 0.921053
236 NZQ 0.473214 0.909091
237 A3S 0.47191 0.810811
238 AMP NAD 0.470588 0.881579
239 SFD 0.46875 0.734043
240 AIR 0.468354 0.901408
241 EEM 0.468085 0.690476
242 AAT 0.468085 0.707317
243 J7V 0.466667 0.833333
244 Z5A 0.466667 0.77907
245 FAY 0.462121 0.8625
246 ETB 0.461538 0.833333
247 A3T 0.461538 0.821918
248 DCA 0.461538 0.823529
249 A6D 0.46 0.722892
250 A U 0.459459 0.87013
251 6K6 0.459184 0.930556
252 GEK 0.459184 0.7375
253 RFL 0.458647 0.821429
254 NAP 0.458333 0.945205
255 S7M 0.458333 0.690476
256 WSA 0.454545 0.788235
257 TAP 0.454545 0.907895
258 FNK 0.454545 0.804598
259 COA 0.453782 0.823529
260 101 0.453488 0.878378
261 NA0 0.45082 0.932432
262 PA7 0.449438 0.708861
263 7RP 0.448276 0.928571
264 GP3 0.446809 0.921053
265 TM1 0.446602 0.77381
266 APU 0.446429 0.894737
267 PUA 0.445378 0.884615
268 V1N 0.443396 0.917808
269 7RA 0.443182 0.957747
270 AMX 0.442623 0.833333
271 COS 0.442623 0.804598
272 CAO 0.442623 0.795455
273 30N 0.442623 0.752688
274 QQY 0.44186 0.815789
275 ACK 0.44186 0.861111
276 0UM 0.44 0.698795
277 NHD 0.439655 0.905405
278 SCO 0.439024 0.823529
279 CMX 0.439024 0.823529
280 GCP 0.438776 0.896104
281 8BR 0.438202 0.906667
282 3AD 0.4375 0.805556
283 GNH 0.4375 0.907895
284 FAM 0.435484 0.804598
285 FCX 0.435484 0.795455
286 ACO 0.435484 0.795455
287 GNP 0.434343 0.896104
288 NMX 0.433071 0.76087
289 MGP 0.43299 0.884615
290 PLP AAD 0.432203 0.741573
291 26A 0.432099 0.763158
292 HAX 0.432 0.804598
293 K15 0.431373 0.682353
294 1DG 0.430894 0.921053
295 DG1 0.430894 0.921053
296 QQX 0.430233 0.805195
297 2VA 0.430108 0.8
298 2MC 0.429688 0.769231
299 FYN 0.428571 0.823529
300 P5F 0.428571 0.823529
301 U G A 0.427481 0.839506
302 RMB 0.426966 0.873239
303 FAI 0.426966 0.916667
304 1RB 0.425287 0.885714
305 SOP 0.425197 0.804598
306 OXK 0.425197 0.804598
307 COK 0.425197 0.804598
308 MCD 0.425197 0.804598
309 CA6 0.425197 0.729167
310 G1R 0.424242 0.907895
311 CC5 0.423077 0.816901
312 NOS 0.423077 0.791667
313 F2N 0.422535 0.813953
314 ANZ 0.422018 0.8
315 CMC 0.421875 0.804598
316 CO6 0.421875 0.804598
317 1VU 0.421875 0.795455
318 GDC 0.420561 0.884615
319 GDD 0.420561 0.884615
320 GKE 0.420561 0.884615
321 NFD 0.420168 0.883117
322 GSP 0.42 0.873418
323 D3Y 0.42 0.789474
324 MC4 0.419847 0.76087
325 3L1 0.419753 0.773333
326 3D1 0.419753 0.773333
327 FA9 0.41958 0.864198
328 G 0.419355 0.906667
329 5GP 0.419355 0.906667
330 SCD 0.418605 0.823529
331 CAJ 0.418605 0.804598
332 CMP 0.417582 0.901408
333 2BA 0.417582 0.915493
334 N01 0.416667 0.905405
335 MLC 0.415385 0.804598
336 3HC 0.415385 0.813953
337 1HE 0.415385 0.786517
338 NMN AMP PO4 0.415254 0.87013
339 2FA 0.414634 0.813333
340 MGO 0.414141 0.860759
341 3NZ 0.413462 0.782051
342 YE1 0.412214 0.813953
343 MCA 0.412214 0.795455
344 CAA 0.412214 0.813953
345 GAV 0.411765 0.884615
346 JLN 0.411111 0.890411
347 P2P 0.411111 0.902778
348 ZZB 0.410256 0.77381
349 CNV FAD 0.410072 0.793103
350 2CP 0.409091 0.795455
351 103 0.409091 0.837838
352 SCA 0.409091 0.804598
353 RP1 0.409091 0.842105
354 SP1 0.409091 0.842105
355 PAX 0.408 0.829268
356 FAD NBT 0.407143 0.75
357 NVA 2AD 0.40625 0.74359
358 IRC 0.406015 0.813953
359 3CP 0.406015 0.804598
360 COW 0.406015 0.795455
361 HGG 0.406015 0.804598
362 BYC 0.406015 0.804598
363 2KQ 0.406015 0.786517
364 COF 0.406015 0.786517
365 CA8 0.406015 0.729167
366 1GZ 0.406015 0.795455
367 G2P 0.405941 0.884615
368 SLU 0.404959 0.770115
369 RBZ 0.404494 0.849315
370 1CZ 0.404412 0.795455
371 FAQ 0.402985 0.804598
372 4CA 0.402985 0.795455
373 BCA 0.402985 0.795455
374 MTP 0.402439 0.730769
375 8OD 0.402062 0.945205
376 CO7 0.401515 0.804598
377 DAL FAD PER 0.401408 0.809524
378 GMV 0.4 0.896104
379 HXC 0.4 0.786517
380 ENQ 0.4 0.916667
381 G2R 0.4 0.884615
382 GRA 0.4 0.804598
Similar Binding Sites
Pocket no: 1; Query (leader) PDB : 16PK; Ligand: BIS; Similar sites found: 34
This union binding pocket (no: 1) in the query (biounit: 16pk.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 16PK BIS 5.476e-20 1
2 4O33 3PG 2.603e-09 0.6281
3 1PHP ADP 6.861e-10 0.51032
4 3ZLB ANP 4.704e-09 0.49885
5 1VPE ANP 7.474e-08 0.49311
6 1QPG MAP 2.135e-07 0.48736
7 3CH6 311 0.04678 0.37298
8 4J36 1HR 0.03179 0.36645
9 1EFV FAD 0.03917 0.34924
10 4QED NAP 0.02947 0.3458
11 1VPE 3PG 2.52e-05 0.33468
12 2P9T 3PG 3.239e-06 0.32851
13 1TLL FMN 0.04969 0.32682
14 3P48 DUP 0.01484 0.31993
15 2FCR FMN 0.02953 0.31915
16 1YOB FMN 0.04599 0.31905
17 1QPG 3PG 4.226e-09 0.31488
18 2AR6 NAG 0.0326 0.31247
19 3P48 DUP 0.0188 0.31187
20 2GUD BMA 0.01282 0.30926
21 3LL2 MAN 0.03033 0.30746
22 4CPZ ZMR 0.04836 0.3063
23 3G89 SAM 0.04225 0.305
24 3K56 IS3 0.04874 0.29536
25 4J51 N75 0.0287 0.2941
26 2B4G ORO 0.03 0.29199
27 2GL9 ASN 0.03331 0.28296
28 2P39 SCR 0.04858 0.28155
29 2D2F ADP 0.01245 0.27732
30 2GNM MAN 0.03455 0.27707
31 2GN3 MAN 0.01336 0.27389
32 2GJP MAL 0.04423 0.2719
33 2GUE NAG 0.03612 0.27
34 3CYQ AMU 0.04104 0.26492
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