Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BIS A:499;
Valid;
none;
submit data
633.276 C15 H22 F4 N5 O12 P3 c1nc(...
EPE A:430;
Invalid;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
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 9 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 5 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 (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
3 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
4 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
5 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
6 5O7D - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
7 2WZC - ALF ADP 3PG n/a n/a
8 5M3U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
12 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
13 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
15 5M1R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
17 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
20 5MXM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
22 2WZD - AF3 ADP 3PG n/a n/a
23 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
24 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
25 2YBE - LA8 ALF 3PG n/a n/a
26 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
27 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
28 5M6Z - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
30 6HXE - 3PG C3 H7 O7 P C([C@H](C(....
31 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
32 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 3ZLB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BIS; Similar ligands found: 325
No: Ligand ECFP6 Tc MDL keys Tc
1 BIS 1 1
2 ATF 0.744444 0.973333
3 A2D 0.72619 0.907895
4 BA3 0.689655 0.907895
5 AP5 0.681818 0.907895
6 ADP 0.681818 0.933333
7 B4P 0.681818 0.907895
8 AT4 0.674157 0.897436
9 AN2 0.674157 0.921053
10 AR6 0.67033 0.907895
11 APR 0.67033 0.907895
12 M33 0.666667 0.896104
13 AD9 0.663043 0.909091
14 HEJ 0.659341 0.933333
15 ACP 0.659341 0.909091
16 ATP 0.659341 0.933333
17 AQP 0.652174 0.933333
18 5FA 0.652174 0.933333
19 A22 0.649485 0.921053
20 ANP 0.648936 0.909091
21 AGS 0.645161 0.886076
22 KG4 0.641304 0.884615
23 PRX 0.634409 0.860759
24 AMP 0.632184 0.906667
25 A 0.632184 0.906667
26 ACQ 0.631579 0.909091
27 ADX 0.630435 0.821429
28 CA0 0.630435 0.884615
29 5SV 0.626263 0.841463
30 50T 0.623656 0.896104
31 HQG 0.622449 0.921053
32 6YZ 0.612245 0.909091
33 ABM 0.611111 0.858974
34 45A 0.611111 0.858974
35 8LE 0.608247 0.839506
36 AMP MG 0.606742 0.868421
37 SRA 0.606742 0.860759
38 A3R 0.60396 0.851852
39 A1R 0.60396 0.851852
40 JNT 0.598039 0.884615
41 AP2 0.597826 0.897436
42 A12 0.597826 0.897436
43 KMQ 0.59434 0.873418
44 25A 0.594059 0.907895
45 OAD 0.592233 0.884615
46 9X8 0.592233 0.8625
47 5AL 0.591837 0.871795
48 25L 0.590476 0.921053
49 ADQ 0.588235 0.884615
50 ADP BEF 0.585106 0.881579
51 ADP MG 0.585106 0.881579
52 APC 0.583333 0.897436
53 TAT 0.581633 0.897436
54 T99 0.581633 0.897436
55 3OD 0.580952 0.884615
56 1ZZ 0.580952 0.833333
57 SRP 0.58 0.85
58 8LH 0.58 0.85
59 AU1 0.578947 0.909091
60 OZV 0.578431 0.907895
61 OMR 0.575221 0.845238
62 PAJ 0.572816 0.831325
63 LAD 0.571429 0.853659
64 QA7 0.568627 0.839506
65 8LQ 0.568627 0.85
66 00A 0.567308 0.875
67 AHX 0.567308 0.841463
68 PTJ 0.566038 0.841463
69 OOB 0.563107 0.871795
70 8QN 0.563107 0.871795
71 ADP PO3 0.561224 0.881579
72 ATP MG 0.561224 0.881579
73 RBY 0.561224 0.873418
74 APC MG 0.561224 0.858974
75 ADV 0.561224 0.873418
76 4AD 0.557692 0.8625
77 AMO 0.557692 0.873418
78 WAQ 0.556604 0.875
79 BEF ADP 0.555556 0.858974
80 ALF ADP 0.554455 0.886076
81 MAP 0.553398 0.886076
82 DLL 0.552381 0.871795
83 TXA 0.551402 0.873418
84 G3A 0.54955 0.864198
85 3UK 0.54717 0.860759
86 XAH 0.545455 0.833333
87 G5P 0.544643 0.864198
88 AFH 0.544643 0.9
89 V2G 0.544554 0.841463
90 L3W 0.543103 0.873418
91 B5V 0.542056 0.85
92 PR8 0.542056 0.843373
93 9SN 0.541284 0.8875
94 4UV 0.540541 0.839506
95 GTA 0.539823 0.833333
96 DQV 0.539823 0.896104
97 VO4 ADP 0.539216 0.884615
98 ANP MG 0.539216 0.871795
99 NAX 0.53913 0.843373
100 NAI 0.53913 0.851852
101 UP5 0.53913 0.8625
102 ME8 0.537037 0.811765
103 FYA 0.537037 0.848101
104 NB8 0.537037 0.841463
105 SON 0.536082 0.873418
106 GAP 0.534653 0.8375
107 48N 0.530435 0.841463
108 ATR 0.53 0.906667
109 4TC 0.529915 0.841463
110 AP0 0.529915 0.841463
111 A2R 0.528846 0.921053
112 LMS 0.526882 0.77907
113 DND 0.525862 0.873418
114 TXD 0.525862 0.851852
115 6V0 0.525862 0.841463
116 ARU 0.523364 0.853659
117 FA5 0.522523 0.85
118 B5Y 0.522523 0.839506
119 B5M 0.522523 0.839506
120 TXE 0.521368 0.851852
121 F2R 0.520661 0.857143
122 9ZD 0.518868 0.851852
123 9ZA 0.518868 0.851852
124 MYR AMP 0.518182 0.811765
125 4UU 0.517544 0.839506
126 GA7 0.517544 0.85
127 139 0.516667 0.821429
128 ADJ 0.516667 0.823529
129 COD 0.516393 0.806818
130 BTX 0.516393 0.835294
131 A4P 0.512605 0.795455
132 BT5 0.512195 0.825581
133 5AS 0.510204 0.736264
134 DAL AMP 0.509434 0.848101
135 LAQ 0.508621 0.833333
136 IOT 0.508333 0.825581
137 2A5 0.504951 0.884615
138 ADP BMA 0.504587 0.860759
139 YLP 0.504274 0.813953
140 UPA 0.504202 0.851852
141 YLB 0.504202 0.813953
142 T5A 0.504132 0.793103
143 PAP 0.5 0.92
144 4UW 0.5 0.809524
145 AOC 0.5 0.769231
146 CNA 0.5 0.873418
147 80F 0.496 0.793103
148 JB6 0.495495 0.851852
149 A4D 0.494382 0.766234
150 RAB 0.494253 0.789474
151 ADN 0.494253 0.789474
152 XYA 0.494253 0.789474
153 YLC 0.491667 0.833333
154 ARG AMP 0.491379 0.823529
155 NA7 0.490909 0.897436
156 7D3 0.489796 0.848101
157 AYB 0.487805 0.804598
158 52H 0.485981 0.736264
159 ITT 0.485149 0.881579
160 7D4 0.485149 0.848101
161 A2P 0.484848 0.893333
162 TYM 0.483333 0.85
163 5N5 0.483146 0.766234
164 ATP A 0.482456 0.87013
165 ATP A A A 0.482456 0.87013
166 JSQ 0.480769 0.960526
167 HFD 0.480769 0.960526
168 G5A 0.480769 0.736264
169 NAD 0.48 0.871795
170 YLA 0.479675 0.813953
171 7MD 0.478632 0.855422
172 AR6 AR6 0.478632 0.858974
173 EP4 0.478261 0.707317
174 5CD 0.477778 0.776316
175 SSA 0.476636 0.755556
176 TAD 0.474576 0.831325
177 A3D 0.472441 0.860759
178 AHZ 0.470588 0.790698
179 A3P 0.47 0.906667
180 NAE 0.469231 0.839506
181 3AM 0.46875 0.868421
182 8X1 0.46789 0.731183
183 53H 0.46789 0.736264
184 TSB 0.46789 0.772727
185 A5A 0.46729 0.761364
186 H1Q 0.466019 0.846154
187 AVV 0.463636 0.911392
188 P1H 0.463235 0.823529
189 7D5 0.463158 0.822785
190 YLY 0.461538 0.804598
191 AMP DBH 0.461538 0.8375
192 ODP 0.460317 0.853659
193 P5A 0.460177 0.741935
194 KAA 0.460177 0.75
195 6RE 0.459184 0.73494
196 AF3 ADP 3PG 0.459016 0.853659
197 ALF ADP 3PG 0.459016 0.853659
198 VMS 0.458716 0.744444
199 NO7 0.458716 0.873418
200 54H 0.458716 0.744444
201 3DH 0.458333 0.725
202 PPS 0.457944 0.821429
203 6AD 0.457944 0.853659
204 DTA 0.457447 0.7375
205 M2T 0.457447 0.690476
206 NVA LMS 0.455357 0.731183
207 7MC 0.455285 0.835294
208 EAD 0.455224 0.821429
209 DSH 0.454545 0.722892
210 5CA 0.454545 0.755556
211 LPA AMP 0.454545 0.811765
212 NAQ 0.454545 0.819277
213 DZD 0.453125 0.831325
214 MTA 0.452632 0.725
215 5X8 0.451923 0.716049
216 ZID 0.451128 0.860759
217 N0B 0.451128 0.813953
218 M24 0.450382 0.865854
219 A3N 0.45 0.7375
220 J7C 0.45 0.743902
221 ZAS 0.44898 0.719512
222 NJP 0.448819 0.886076
223 V3L 0.448598 0.907895
224 NSS 0.446429 0.755556
225 LSS 0.446429 0.72043
226 DSZ 0.446429 0.755556
227 GJV 0.445545 0.746988
228 S4M 0.445545 0.666667
229 NAD IBO 0.443548 0.858974
230 NAD TDB 0.443548 0.858974
231 9K8 0.443478 0.731183
232 2AM 0.443299 0.881579
233 SFD 0.440559 0.69697
234 AV2 0.440367 0.858974
235 38V 0.440298 0.833333
236 9JJ 0.44 0.878049
237 FDA 0.439716 0.786517
238 LEU LMS 0.438596 0.691489
239 PO4 PO4 A A A A PO4 0.438596 0.844156
240 SFG 0.438095 0.725
241 CUU 0.438095 0.907895
242 6FA 0.43662 0.793103
243 D4F 0.43609 0.790698
244 NDC 0.435714 0.864198
245 FB0 0.435714 0.8
246 IMO 0.435644 0.868421
247 3AT 0.435185 0.907895
248 NAJ PZO 0.435115 0.797619
249 GSU 0.434783 0.755556
250 4TA 0.434109 0.761364
251 0WD 0.434109 0.864198
252 NDP 0.433071 0.864198
253 NPW 0.433071 0.855422
254 NDE 0.431655 0.873418
255 6MZ 0.431373 0.87013
256 EEM 0.431193 0.670455
257 FAS 0.430556 0.802326
258 FAD 0.430556 0.802326
259 OVE 0.43 0.848101
260 NZQ 0.429688 0.853659
261 TXP 0.429688 0.864198
262 YSA 0.428571 0.736264
263 LQJ 0.428571 0.858974
264 B1U 0.428571 0.697917
265 62F 0.428571 0.811765
266 MAO 0.427184 0.735632
267 O02 0.425926 0.864198
268 FAY 0.425676 0.811765
269 P5F 0.424837 0.777778
270 DAT 0.424528 0.848101
271 649 0.424 0.741935
272 AMP NAD 0.423077 0.848101
273 5AD 0.422222 0.697368
274 DTP 0.422018 0.848101
275 7C5 0.421488 0.768293
276 8PZ 0.420168 0.755556
277 7DD 0.419048 0.92
278 FNK 0.418919 0.76087
279 SA8 0.416667 0.686047
280 A5D 0.416667 0.7375
281 MHZ 0.415094 0.696629
282 NWW 0.414894 0.710526
283 0T1 0.414815 0.818182
284 4YB 0.414634 0.73913
285 RFL 0.413333 0.775281
286 SAH 0.412844 0.719512
287 SAI 0.412844 0.710843
288 6C6 0.412844 0.873418
289 XNP 0.412214 0.843373
290 NAJ PYZ 0.411765 0.802326
291 FAJ 0.411392 0.784091
292 MCD 0.411348 0.8
293 S7M 0.410714 0.670455
294 DCA 0.410448 0.797753
295 ETB 0.410448 0.806818
296 FCX 0.410072 0.852273
297 FAM 0.410072 0.862069
298 NIA 0.41 0.77381
299 6IA 0.409091 0.809524
300 0UM 0.408696 0.697674
301 K3K 0.408333 0.753086
302 7DT 0.407407 0.92
303 APU 0.40625 0.839506
304 Z5A 0.405797 0.736264
305 30N 0.405797 0.75
306 AMX 0.405797 0.827586
307 A7D 0.40566 0.75
308 AAT 0.405405 0.705882
309 128 0.404762 0.733333
310 COA 0.404412 0.818182
311 Y3J 0.404255 0.746667
312 GGZ 0.403509 0.776471
313 7L1 0.402878 0.791209
314 SCO 0.402878 0.818182
315 CMX 0.402878 0.818182
316 2SA 0.401786 0.873418
317 K15 0.401709 0.681818
318 A6D 0.401709 0.681818
319 K3E 0.401639 0.743902
320 WSA 0.401575 0.744444
321 CA6 0.401408 0.727273
322 12D 0.4 0.741573
323 NWQ 0.4 0.692308
324 71V 0.4 0.851852
325 6K6 0.4 0.87013
Similar Ligands (3D)
Ligand no: 1; Ligand: BIS; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 16PK; Ligand: BIS; 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: 16pk.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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