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Receptor
PDB id Resolution Class Description Source Keywords
1KC7 2.2 Å EC: 2.7.9.1 PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PHOSPHONOPYRUVATE CLOSTRIDIUM SYMBIOSUM TRANSFERASE PHOSPHOTRANSFERASE KINASE PHOSPHONOPYRUVATE I
Ref.: PYRUVATE SITE OF PYRUVATE PHOSPHATE DIKINASE: CRYST STRUCTURE OF THE ENZYME-PHOSPHONOPYRUVATE COMPLEX, MUTANT ANALYSIS BIOCHEMISTRY V. 41 780 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:1001;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PPR A:1000;
Valid;
none;
Ki = 3 uM
168.042 C3 H5 O6 P C(C(=...
SO4 A:1002;
A:1003;
A:1004;
A:1005;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KC7 2.2 Å EC: 2.7.9.1 PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PHOSPHONOPYRUVATE CLOSTRIDIUM SYMBIOSUM TRANSFERASE PHOSPHOTRANSFERASE KINASE PHOSPHONOPYRUVATE I
Ref.: PYRUVATE SITE OF PYRUVATE PHOSPHATE DIKINASE: CRYST STRUCTURE OF THE ENZYME-PHOSPHONOPYRUVATE COMPLEX, MUTANT ANALYSIS BIOCHEMISTRY V. 41 780 2002
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KC7 Ki = 3 uM PPR C3 H5 O6 P C(C(=O)C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1KC7 Ki = 3 uM PPR C3 H5 O6 P C(C(=O)C(=....
2 1VBH - PEP C3 H5 O6 P C=C(C(=O)O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1KC7 Ki = 3 uM PPR C3 H5 O6 P C(C(=O)C(=....
2 1VBH - PEP C3 H5 O6 P C=C(C(=O)O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PPR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PPR 1 1
2 PAE 0.571429 0.866667
3 DCO 0.5 0.722222
4 KPA 0.5 0.875
5 7VD 0.478261 0.806452
6 HPV 0.413793 0.903226
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KC7; Ligand: PPR; Similar sites found with APoc: 442
This union binding pocket(no: 1) in the query (biounit: 1kc7.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 4UAI 3GG None
2 6C6O ENG 1.07962
3 6F90 MVL 1.37552
4 1ZCB GDP 1.38122
5 2NCD ADP 1.42857
6 5XDR ADP 1.44928
7 5ZXD ATP 1.4652
8 5XET ME8 1.51229
9 2OJW ADP 1.5625
10 1ZGS XMM 1.566
11 1QO8 FAD 1.59011
12 1Q19 SSC 1.59046
13 3NEM AMO 1.59817
14 4PJ3 ANP 1.60367
15 2ZPA ADP 1.63934
16 2BD0 NAP 1.63934
17 1WD4 AHR 1.65975
18 4U7W NDP 1.66667
19 6FP4 FAD 1.67224
20 5NDF LU2 1.75131
21 5NDF UDP 1.75131
22 3HQP OXL 1.80361
23 1W96 S1A 1.80505
24 2Z49 AMG 1.85185
25 2Z48 A2G 1.85185
26 5JBE GLC GLC GLC GLC GLC 1.87354
27 1UPA TPP 1.91972
28 2IHU TP9 1.91972
29 2IHT TPP 1.91972
30 5WKC TP9 1.92024
31 1QFY FAD 1.94805
32 1QFY NAP 1.94805
33 4WZ8 3W7 1.95059
34 3MAG SAH 1.9544
35 2YIC TPP 1.95853
36 1ZPT FAD 1.97368
37 2WPF WPF 2.0202
38 2WPF FAD 2.0202
39 3NVD OAN 2.02492
40 2DBZ NAP 2.09581
41 6BII NAP 2.1021
42 2OO0 PLP 2.12314
43 3W8X FTK 2.13675
44 3W8X FAD 2.13675
45 4PNI KQQ 2.13904
46 1AFS NAP 2.16718
47 5WRI A3P 2.1875
48 2GKS ADP 2.1978
49 4HCX NDP 2.20049
50 3H4T UDP 2.22772
51 2NPX FAD 2.23714
52 1KOR ARG 2.25
53 1KOR SIN 2.25
54 1P9B GDP 2.26244
55 1DUB CAA 2.29885
56 4W6Z 8ID 2.30548
57 5WRJ A3P 2.31023
58 4OHY ANP 2.32019
59 5ZYN FAD 2.33546
60 5C03 AGS 2.33918
61 6F92 MVL 2.35602
62 2PO3 T4K 2.35849
63 5TIV A3P 2.37154
64 4B7X NAP 2.38095
65 1P72 ADP 2.39521
66 1PZ1 NAP 2.4024
67 1PIG AGL GLC HMC AGL GLC BGC 2.41935
68 5GSN NAP 2.42826
69 5GSN FAD 2.42826
70 1VKJ A3P 2.45614
71 1ZQ9 SAM 2.45614
72 4UXL 5P8 2.48447
73 1WVG APR 2.50696
74 5U6C 7YS 2.53968
75 2H04 4UN 2.55591
76 1ORR NAD 2.59366
77 1P7T PYR 2.59918
78 2BGS NDP 2.61628
79 3RUU 37G 2.62009
80 1D8C GLV 2.62794
81 5VZ0 2BA 2.63459
82 4L9Z COA 2.65487
83 4L9Z OXL 2.65487
84 5FAW CHT 2.69939
85 3BFX A3P 2.7027
86 3QVV A3P 2.71186
87 6A1G 9OL 2.77778
88 4PFO ADP 2.79188
89 2FNA ADP 2.80112
90 5GM9 CBK 2.8169
91 4G9E C4L 2.86738
92 1UWK NAD 2.87253
93 1UWK URO 2.87253
94 1NHX PEP 2.88
95 1NHX FTB 2.88
96 2VSU ACO 2.90909
97 3ZOK NAD 2.91005
98 5O4J 9KH 2.91971
99 5O4J PJL 2.91971
100 5O4J SAH 2.91971
101 4PFT MAB 2.94118
102 5GVL GI8 2.94118
103 5GVL PLG 2.94118
104 2YCJ C2F 2.95203
105 3H7U NAP 2.98507
106 3BAZ NAP 3.003
107 2CUL FAD 3.01724
108 3EUF BAU 3.04878
109 3B1Q NOS 3.06748
110 1SVK ALF GDP 3.11615
111 1RP0 AHZ 3.16901
112 6A3J NAI 3.17073
113 6A3J SOE 3.17073
114 2WW4 ADP 3.18021
115 1ZGD NAP 3.20513
116 3WV8 ATP 3.21101
117 5UXF 2BA 3.21637
118 2XAU ADP 3.23415
119 3WG6 NDP 3.25733
120 2D4V NAD 3.2634
121 5N6C NAD 3.33333
122 5H81 NAP 3.3419
123 1Y3A GDP 3.34347
124 1D6H COA 3.35917
125 3EAU PDN 3.36391
126 3EAU NDP 3.36391
127 3CV2 OXL 3.38346
128 4PVV HO4 3.39506
129 3QM1 ZYC 3.39623
130 2B9F ADP 3.39943
131 2B9H ADP 3.39943
132 4KCT PYR 3.40681
133 2F6U CIT 3.4188
134 3MGB PAP 3.44828
135 5WC2 ADP 3.47222
136 1EE0 CAA 3.48259
137 3G5D 1N1 3.4965
138 4D7E FAD 3.4965
139 1FK8 NAD 3.50195
140 3WQT ANP 3.5124
141 5E5U MLI 3.51759
142 5N69 ADP 3.51759
143 4IXW IXW 3.54331
144 1MJH ATP 3.55097
145 2C42 PYR 3.55097
146 2C42 TPP 3.55097
147 6C4N NAP 3.56347
148 4RVU NDP 3.61446
149 2C49 ADN 3.64238
150 2OAT PFM 3.64465
151 3A4T SFG 3.64964
152 2GWH A3P 3.69128
153 1VP5 NAP 3.69128
154 1X8J A3P 3.7037
155 3MCT SAH 3.7037
156 1JE1 GMP 3.81356
157 2Z6D FMN 3.84615
158 1VA6 P2S 3.861
159 1VA6 ADP 3.861
160 1V1A KDG 3.8835
161 3KRB NAP 3.89222
162 5XVH NAP 3.92157
163 2C9O ADP 3.94737
164 2G50 PYR 3.96226
165 2PVN P63 3.97727
166 3JYN NDP 4
167 3PY5 AMP 4.0146
168 4HA9 NDP 4.01606
169 3I54 CMP 4.01606
170 4IP7 FLC 4.05157
171 1H74 ADP 4.05405
172 1H74 ILE 4.05405
173 3MVH WFE 4.09357
174 5BJX NAD 4.09836
175 5BJX UDP 4.09836
176 1BZL GCG 4.11523
177 1N9G NAP 4.14508
178 5O3Q CMP 4.16667
179 4Z87 5GP 4.19048
180 2I8T GDD 4.19162
181 1LVK MNT BEF 4.19948
182 5LTJ ADP 4.20168
183 6D6Y SAH 4.2065
184 3KVY URA 4.20712
185 4Y85 499 4.21687
186 1OXV ANP 4.24929
187 1W78 PD8 4.2654
188 1W78 ADP 4.2654
189 4NST ADP 4.2735
190 5EFQ ADP 4.32277
191 2QZS GLC 4.3299
192 2QZS ADP 4.3299
193 2QZS 250 4.3299
194 6F5W KG1 4.33604
195 1LLU NAD 4.38596
196 3UYK 0CX 4.39277
197 1NY5 ADP 4.39277
198 5UIV ADP 4.40529
199 1C9K 5GP 4.44444
200 2HJ4 PNZ 4.44444
201 5OCM NAP 4.46735
202 4KQ6 DLZ 4.46927
203 5WX3 COA 4.54545
204 2FLI DX5 4.54545
205 2YAK OSV 4.5614
206 2NVA PL2 4.56989
207 5VHC BEF ADP 4.5977
208 3CV7 NAP 4.61538
209 3CV7 C2U 4.61538
210 3KCC CMP 4.61538
211 4YRY FAD 4.71014
212 1AQU A3P 4.7138
213 5VOP C2F 4.72973
214 6FAA ADP 4.73282
215 3EYA TDP 4.73588
216 3IID APR 4.73934
217 5U5G NAP 4.74576
218 1G3M PCQ 4.7619
219 1G3M A3P 4.7619
220 1EKO NAP 4.7619
221 1EKO I84 4.7619
222 2VHW NAI 4.77454
223 1PZG A3D 4.83384
224 4J7U YTZ 4.86111
225 4J7U NAP 4.86111
226 1F9V ADP 4.89914
227 5A0U CHT 4.90566
228 4Z94 ATP 4.90798
229 2CI5 HCS 4.92958
230 2WN6 NDP 4.9676
231 1T36 U 4.97382
232 1T36 ADP 4.97382
233 5I0H ADP BEF 4.99325
234 4AT3 LTI 5.01672
235 4A4X JUP 5.01792
236 1P1C SAH 5.02513
237 1KYV RBF 5.03145
238 1ZGA SAH 5.04202
239 1DL5 SAH 5.04732
240 3C0G 3AM 5.12821
241 4K49 HFQ 5.14706
242 3DZD ADP 5.16304
243 1SOW NAD 5.18293
244 1LQA NDP 5.20231
245 4BNU 9KQ 5.20446
246 1BG2 ADP 5.23077
247 4ZG4 VO4 ADP 5.2356
248 1R6W 164 5.2795
249 6FYZ EBE 5.31646
250 4WOP CTP 5.33333
251 4JR7 GNP 5.34759
252 3BD9 A3P 5.35714
253 4PLG OXM 5.38922
254 4PLG NAI 5.38922
255 5NMX FAD 5.41176
256 3BZ3 YAM 5.43478
257 3TWO NDP 5.45977
258 6GBV FMN 5.47945
259 2UUU FAD 5.47945
260 3C6K MTA 5.51181
261 3C6K SPD 5.51181
262 1H65 GDP 5.55556
263 2BP1 NDP 5.55556
264 4XTX 590 5.55556
265 2NZ5 226 5.56901
266 2J3M PRI 5.59441
267 2BSA NAP 5.61056
268 2BSA FAD 5.61056
269 4TR9 ASP TRP ASN 5.69106
270 4FJU NAI 5.69801
271 4FJU GLV 5.69801
272 2X1L ADN 5.72519
273 2NU5 NAG 5.7377
274 4GC1 MAN MAN 5.7971
275 2XVF FAD 5.81897
276 4USI AKG 5.84416
277 1KRR ACO 5.91133
278 2A92 NAI 5.919
279 6AU6 GDP 6.1008
280 1JQN DCO 6.11552
281 3HGM ATP 6.12245
282 3UWV 2PG 6.13027
283 1VM6 NAD 6.14035
284 1WK9 TSB 6.16438
285 3H11 ALA ILE GLU THR ASA 6.27306
286 4R3U 3KK 6.32911
287 4R3U 3HC 6.32911
288 4XO8 KGM 6.32911
289 1Q8Q MAN MMA 6.34921
290 1Q8S MAN MMA 6.34921
291 1Q8P MAN MMA 6.34921
292 5A6N U7E 6.36042
293 4CQK PIO 6.38298
294 5K3W PLP 6.38978
295 1VHT BA3 6.42202
296 5JFS 6K0 6.49351
297 5F5N NAD 6.57439
298 1KYZ SAH 6.57534
299 1T8U A3P 6.61765
300 1Q20 PLO 6.68896
301 1Q20 A3P 6.68896
302 2VB6 ADP BEF 6.71141
303 5A5W GUO 6.71937
304 3ALN ANP 6.72783
305 1MO9 KPC 6.88337
306 1MO9 FAD 6.88337
307 3CX8 GSP 6.89655
308 1UY4 XYP XYP XYP XYP 6.89655
309 1ZUA TOL 6.94006
310 1ZUA NAP 6.94006
311 3O3R NAP 6.96203
312 3Q9N COA 6.96203
313 2Z6C FMN 6.97674
314 1FRB ZST 6.98413
315 5EXW 7DT 7
316 1NZY BCA 7.0632
317 4OIT BMA 7.07965
318 4OIT MAN 7.07965
319 2Q46 NAP 7.11462
320 4R38 RBF 7.14286
321 3DLS ADP 7.16418
322 2RDE C2E 7.17131
323 5JBX COA 7.27969
324 1KJ1 MAN 7.33945
325 2CFA FAD 7.37327
326 3ZFD ANP 7.40741
327 1VBJ NAP 7.47331
328 1J99 AND 7.50853
329 2ZEJ GDP 7.6087
330 5EXE 5SR 7.61905
331 5ZZ6 NAD 7.69231
332 3CV6 NAP 7.73994
333 5EH0 5NW 7.75194
334 1JJV ATP 7.76699
335 2EXX NAP 7.84314
336 4CVN ADP 7.8534
337 5HIP 61O 7.92079
338 2TPS TPS 7.92952
339 1IZC PYR 7.9646
340 6F8B CXH 7.97342
341 2PUL ACP 8.06045
342 4HEQ FMN 8.21918
343 1G16 GDP 8.23529
344 2F59 INI 8.28025
345 5VKT NAP 8.28729
346 3H4S ADP 8.29016
347 1SAY PYR 8.31025
348 3IS2 FAD 8.44156
349 1GP2 GDP 8.4507
350 1M7G AV2 8.53081
351 1M7G ADX 8.53081
352 2VWT PYR 8.61423
353 4UTG ANP 8.67052
354 4L2I FAD 8.74525
355 4L2I NAD 8.74525
356 3WCZ NAP 8.76623
357 4XYM A12 8.83621
358 6CRK GDP 8.88031
359 4BVA NDP 8.95522
360 4BVA T3 8.95522
361 3WCA FPS 9.0411
362 5C8W PCG 9.09091
363 2D3M COA 9.1133
364 5DK4 ATP 9.11854
365 5DK4 5BX 9.11854
366 4P5Z Q7M 9.14127
367 1PA9 CSN 9.15493
368 4OH4 ANP 9.30931
369 1WAP TRP 9.33333
370 3D72 FAD 9.39597
371 5EOB 5QQ 9.40439
372 2C91 NAP 9.46746
373 1YQD NAP 9.56284
374 1KQN NAD 9.67742
375 5VAD 91Y 9.68992
376 1YRO GDU 9.7561
377 2QV7 ADP 9.79228
378 5FI3 NAP 9.80392
379 5Y2W PGA 9.82906
380 2PID YSA 9.83146
381 5EY0 GTP 9.85401
382 1IUP ALQ 9.92908
383 3GDH SAH 9.95851
384 3V8S 0HD 10
385 1P0H ACO 10.0629
386 4JTA NAP 10.1167
387 2NP9 YE1 10.2273
388 3KJQ B94 10.3659
389 1EXB NDP 10.6796
390 1C1X NAD 10.7042
391 1AKV FMN 10.8844
392 4YSX FAD 10.8974
393 1E6E FAD 10.9375
394 1KK8 BEF ADP 11.6883
395 4LIK CIT 11.7347
396 4TWP AXI 11.8081
397 4YMU ATP 12.0833
398 1D2N ANP 12.1324
399 3NRZ FAD 12.1951
400 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 12.2605
401 4XDA ADP 12.2977
402 3GNI ATP 12.5964
403 4QOS ADP 12.8302
404 5TBS ADE 12.892
405 3TKY SAH 13.0435
406 3CAQ NDP 13.1902
407 3GE7 AFQ 13.2124
408 1W0J ADP 13.6029
409 1V2G OCA 13.6842
410 3ZZS TRP 13.8462
411 5WS9 ATP 14.7368
412 5WS9 OXL 14.7368
413 6GG9 FMN 14.8148
414 5DJT FMN 15.1724
415 5DJU FMN 15.1724
416 3TA2 AKG 15.2542
417 5AZ1 NDP 15.2975
418 2V5K OXM 15.331
419 4C5N ACP 15.5797
420 4C5N PXL 15.5797
421 4R2M ANP 15.8228
422 2D5A COA 15.9722
423 4IJR NDP 16.2791
424 4H3P ANP 16.8508
425 4TMK T5A 16.9014
426 2KIN ADP 17
427 4IEN GDP 17.1779
428 4B5W PYR 17.1875
429 6G9I CXX 17.8571
430 2V7Q ATP 18
431 2CK3 ANP 18
432 5SVV FMN 18.2482
433 4L80 OXL 20.6897
434 1EJB INJ 20.8333
435 2C94 TSF 21.25
436 1XTT U5P 21.7593
437 2F5Z FAD 21.875
438 5A89 FMN 23.7179
439 5A89 ADP 23.7179
440 2Y65 ADP 30
441 4CYD CMP 33.3333
442 2XZ9 PYR 47.8395
Pocket No.: 2; Query (leader) PDB : 1KC7; Ligand: PPR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1kc7.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1KC7; Ligand: PPR; Similar sites found with APoc: 20
This union binding pocket(no: 3) in the query (biounit: 1kc7.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z6T ADP 1.18443
2 4P53 NAI 1.42857
3 1MUU NAD 1.6055
4 5GXU FAD 2.52005
5 1YKF NAP 2.55682
6 1LUA NAP 2.78746
7 4GKV NAD 2.97619
8 2IO8 ADP 3.06947
9 6F3M ADN 3.69565
10 5ABH YWN 3.71901
11 3DAK ANP 3.7931
12 2A42 ATP 3.84615
13 3C3N FMN 3.84615
14 5MEX PAP 4.34783
15 2A19 ANP 6.33803
16 3V2U ATP 7.30594
17 5TPR NAD 7.43243
18 4XT8 NAP 7.75194
19 3OVR 5SP 8.33333
20 4LOO SB4 11.3573
Pocket No.: 4; Query (leader) PDB : 1KC7; Ligand: PPR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1kc7.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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