Receptor
PDB id Resolution Class Description Source Keywords
6JO3 2.35 Å EC: 2.5.1.41 CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHAT FROM THERMOPLASMA ACIDOPHILUM IN COMPLEX WITH SUBSTRATE SN-1 -PHOSPHATE THERMOPLASMA ACIDOPHILUM DSM 1728 ARCHAEA ETHER LIPID THERMOPLASMA TRANSFERASE STRUCTURAL
Ref.: CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE FROM THERMOPLASMA ACIDOPHILUM IN WITH THE SUBSTRATE SN-GLYCEROL 1-PHOSPHATE. ACTA CRYSTALLOGR.,SECT.F V. 75 470 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1GP A:501;
 Valid;
 none;
 submit data
172.074 C3 H9 O6 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6JO3 2.35 Å EC: 2.5.1.41 CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHAT FROM THERMOPLASMA ACIDOPHILUM IN COMPLEX WITH SUBSTRATE SN-1 -PHOSPHATE THERMOPLASMA ACIDOPHILUM DSM 1728 ARCHAEA ETHER LIPID THERMOPLASMA TRANSFERASE STRUCTURAL
Ref.: CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE FROM THERMOPLASMA ACIDOPHILUM IN WITH THE SUBSTRATE SN-GLYCEROL 1-PHOSPHATE. ACTA CRYSTALLOGR.,SECT.F V. 75 470 2019
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6JO3 - 1GP C3 H9 O6 P C([C@@H](C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6JO3 - 1GP C3 H9 O6 P C([C@@H](C....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 4JEJ - 1GP C3 H9 O6 P C([C@@H](C....
2 6JO3 - 1GP C3 H9 O6 P C([C@@H](C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 1GP; Similar ligands found: 28
No: Ligand ECFP6 Tc MDL keys Tc
1 G3P 1 1
2 1GP 1 1
3 GP9 0.551724 0.90625
4 GPE 0.514286 0.731707
5 GOS 0.5 0.882353
6 M2P 0.5 0.882353
7 DX5 0.484848 0.911765
8 LX1 0.484848 0.828571
9 A5P 0.484848 0.911765
10 LXP 0.484848 0.911765
11 PSE 0.483871 0.736842
12 HG3 0.482759 0.90625
13 S6P 0.470588 0.939394
14 DXP 0.457143 0.828571
15 G3H 0.4375 0.848485
16 3PG 0.4375 0.852941
17 D5X 0.432432 0.805556
18 CH5 0.425 0.6
19 EFS 0.423077 0.69697
20 AGP 0.421053 0.756098
21 M6R 0.421053 0.756098
22 GSE 0.414634 0.714286
23 E4P 0.411765 0.878788
24 R52 0.405405 0.828571
25 DG6 0.405405 0.885714
26 TX4 0.405405 0.630435
27 R5P 0.405405 0.828571
28 FQ8 0.4 0.885714
Similar Ligands (3D)
Ligand no: 1; Ligand: 1GP; Similar ligands found: 523
No: Ligand Similarity coefficient
1 PGA 1.0000
2 13P 1.0000
3 X1S 0.9987
4 PGH 0.9917
5 LTL 0.9827
6 3PP 0.9751
7 129 0.9655
8 PEP 0.9647
9 1SH 0.9644
10 CYX 0.9637
11 FUM 0.9535
12 3SL 0.9510
13 SIN 0.9503
14 PPR 0.9497
15 LLQ 0.9494
16 PIS 0.9486
17 HX2 0.9483
18 SPV 0.9474
19 PMB 0.9470
20 GLU 0.9442
21 4MV 0.9433
22 KVV 0.9431
23 GZ3 0.9428
24 A20 0.9411
25 2PN 0.9407
26 GPJ 0.9402
27 AKG 0.9401
28 FB2 0.9400
29 1SA 0.9391
30 PPV 0.9382
31 OPE 0.9379
32 GPF 0.9370
33 HPV 0.9363
34 AT3 0.9356
35 H95 0.9353
36 POP 0.9352
37 2PG 0.9349
38 SEP 0.9342
39 OGA 0.9340
40 7VD 0.9331
41 LUQ 0.9329
42 IP8 0.9308
43 PAH 0.9301
44 PEQ 0.9301
45 LMR 0.9297
46 MDN 0.9293
47 RTK 0.9292
48 GLY GLY 0.9290
49 0V5 0.9290
50 4LR 0.9282
51 ICF 0.9281
52 8K2 0.9281
53 OSE 0.9265
54 ACH 0.9264
55 PCT 0.9264
56 51R 0.9263
57 KVP 0.9257
58 CCE 0.9257
59 HMS 0.9247
60 DQY 0.9247
61 NMG 0.9241
62 3S5 0.9241
63 CCD 0.9232
64 SAN 0.9231
65 AL0 0.9228
66 DGL 0.9227
67 OKG 0.9226
68 QMP 0.9221
69 MEQ 0.9215
70 XCZ 0.9213
71 CHH 0.9211
72 PLU 0.9209
73 NM3 0.9204
74 NF3 0.9201
75 SHF 0.9187
76 FOM 0.9185
77 ASP 0.9185
78 2HG 0.9181
79 EHM 0.9178
80 MLT 0.9177
81 DE5 0.9175
82 MHN 0.9172
83 ZGL 0.9172
84 G2H 0.9166
85 PC 0.9165
86 COM 0.9164
87 TSU 0.9164
88 HPS 0.9162
89 MAE 0.9162
90 DGN 0.9159
91 AG2 0.9158
92 7OD 0.9157
93 3OL 0.9157
94 1DV 0.9155
95 FBW 0.9154
96 GLN 0.9150
97 6PC 0.9150
98 VKC 0.9149
99 MUC 0.9149
100 OAA 0.9147
101 9J3 0.9146
102 FB1 0.9146
103 N6C 0.9145
104 ACA 0.9144
105 9GB 0.9142
106 PAE 0.9141
107 BEZ 0.9138
108 HBU 0.9135
109 SHV 0.9134
110 152 0.9129
111 DIR 0.9128
112 TB6 0.9128
113 HSO 0.9127
114 SS2 0.9127
115 FCR 0.9126
116 DHM 0.9124
117 AMS 0.9123
118 HL5 0.9121
119 PMF 0.9121
120 SRT 0.9117
121 S0H 0.9116
122 MSL 0.9116
123 9ON 0.9112
124 FOC 0.9110
125 9X6 0.9104
126 URQ 0.9100
127 FCN 0.9099
128 4J8 0.9089
129 GUA 0.9085
130 7BC 0.9081
131 SAT 0.9080
132 3OC 0.9080
133 KMH 0.9077
134 2IT 0.9075
135 FBV 0.9075
136 0VT 0.9073
137 GGL 0.9073
138 TAU 0.9072
139 ORN 0.9071
140 ABU 0.9070
141 5XA 0.9067
142 FBS 0.9067
143 P22 0.9065
144 SD4 0.9065
145 TLA 0.9065
146 XRG 0.9065
147 A09 0.9064
148 BNS 0.9063
149 LEU 0.9062
150 1DQ 0.9061
151 FBU 0.9059
152 HIS 0.9058
153 CRN 0.9057
154 NSB 0.9057
155 OVV 0.9056
156 DLY 0.9056
157 2RH 0.9056
158 UYA 0.9055
159 BEN 0.9054
160 LYS 0.9053
161 COI 0.9053
162 PBC 0.9052
163 7WG 0.9051
164 HTX 0.9050
165 TEO 0.9048
166 OK7 0.9048
167 A13 0.9047
168 BHH 0.9045
169 CP 0.9043
170 KPC 0.9040
171 B85 0.9037
172 S2G 0.9035
173 PG0 0.9034
174 MPD 0.9031
175 XYL 0.9031
176 HPN 0.9028
177 ASN 0.9026
178 PAC 0.9026
179 4CS 0.9025
180 NPO 0.9025
181 DAS 0.9021
182 98J 0.9020
183 KQY 0.9020
184 LEA 0.9019
185 3LR 0.9018
186 QY9 0.9018
187 DS0 0.9017
188 ONL 0.9016
189 AAS 0.9015
190 OEG 0.9012
191 BAM 0.9012
192 EOU 0.9010
193 6NA 0.9010
194 URP 0.9006
195 3NT 0.9006
196 XLS 0.9001
197 VGL 0.8996
198 3OM 0.8994
199 MJ2 0.8992
200 GVM 0.8991
201 CFI 0.8991
202 3HB 0.8991
203 SYC 0.8989
204 ISZ 0.8987
205 PHB 0.8986
206 THE 0.8986
207 SVD 0.8984
208 NIO 0.8984
209 SPA 0.8983
210 TAR 0.8983
211 3YP 0.8982
212 RHU 0.8978
213 NCA 0.8978
214 PAB 0.8977
215 GWM 0.8976
216 SSN 0.8973
217 PCA 0.8973
218 PZI 0.8972
219 NLP 0.8971
220 NIZ 0.8971
221 AC6 0.8970
222 K6V 0.8970
223 RNT 0.8969
224 GAB 0.8969
225 ILE 0.8969
226 EDR 0.8968
227 DHI 0.8967
228 8GL 0.8966
229 K6H 0.8966
230 GJZ 0.8965
231 DAV 0.8964
232 NLE 0.8961
233 GOJ 0.8961
234 XM0 0.8961
235 53C 0.8959
236 K5W 0.8958
237 MNN 0.8957
238 RMN 0.8955
239 IXW 0.8953
240 NTN 0.8952
241 ROR 0.8950
242 HSE 0.8949
243 LYN 0.8944
244 P7I 0.8943
245 GLY ALA 0.8943
246 LNO 0.8942
247 HIC 0.8940
248 7N0 0.8938
249 IZC 0.8936
250 GG6 0.8934
251 GRO 0.8933
252 BHO 0.8931
253 RB5 0.8930
254 40E 0.8928
255 SG3 0.8928
256 IFP 0.8926
257 S8V 0.8925
258 ETM 0.8923
259 3AB 0.8923
260 PG3 0.8918
261 PZA 0.8918
262 MPH 0.8917
263 HGA 0.8916
264 IHG 0.8915
265 J9N 0.8915
266 FBM 0.8913
267 M6W 0.8912
268 1DJ 0.8911
269 HYA 0.8910
270 DMV 0.8909
271 NBZ 0.8909
272 F9P 0.8909
273 RSO 0.8909
274 RB0 0.8907
275 DYT 0.8907
276 TPO 0.8905
277 ALA ALA 0.8904
278 UNU 0.8904
279 K34 0.8903
280 RNS 0.8903
281 DAL DAL 0.8902
282 3BU 0.8899
283 SHO 0.8898
284 J9T 0.8897
285 2FT 0.8896
286 2EH 0.8896
287 5FX 0.8895
288 6JN 0.8890
289 3BZ 0.8890
290 MZT 0.8889
291 X1R 0.8889
292 PSJ 0.8889
293 URO 0.8888
294 FAN 0.8888
295 FQI 0.8887
296 MHO 0.8886
297 IOM 0.8886
298 FBJ 0.8886
299 NXA 0.8884
300 2CO 0.8884
301 YCP 0.8883
302 SS1 0.8881
303 51F 0.8880
304 CHT 0.8880
305 DZA 0.8880
306 MXN 0.8879
307 CXF 0.8879
308 FEH 0.8877
309 XBT 0.8877
310 2AS 0.8877
311 XUL 0.8876
312 MTL 0.8875
313 PRO 0.8874
314 TP5 0.8873
315 DYA 0.8872
316 B3U 0.8870
317 X0V 0.8870
318 ORO 0.8870
319 AOS 0.8869
320 16D 0.8869
321 ZBT 0.8869
322 TZL 0.8869
323 DOR 0.8866
324 JYD 0.8864
325 HQJ 0.8862
326 CIZ 0.8860
327 9YL 0.8850
328 ONH 0.8850
329 9SB 0.8849
330 HCS 0.8849
331 TIH 0.8848
332 RUJ 0.8848
333 DCL 0.8848
334 6OT 0.8848
335 NFA 0.8847
336 HHI 0.8846
337 UGC 0.8844
338 GLY CYS 0.8844
339 AHB 0.8844
340 WCE 0.8844
341 OCT 0.8842
342 ITN 0.8842
343 3FH 0.8841
344 069 0.8841
345 6M4 0.8839
346 R9M 0.8837
347 PHE 0.8837
348 LFC 0.8836
349 EKZ 0.8836
350 MRZ 0.8835
351 POA 0.8835
352 2HE 0.8835
353 TPA 0.8834
354 PHU 0.8834
355 HBD 0.8834
356 49F 0.8828
357 M4S 0.8826
358 4SX 0.8824
359 HY1 0.8824
360 Q07 0.8822
361 HZP 0.8821
362 173 0.8820
363 SMN 0.8819
364 I4B 0.8818
365 8X3 0.8817
366 MEV 0.8815
367 271 0.8812
368 14J 0.8811
369 RBL 0.8811
370 HFA 0.8810
371 R67 0.8809
372 HIO 0.8809
373 TAG 0.8804
374 HYP 0.8801
375 7C3 0.8801
376 UY7 0.8798
377 SOR 0.8796
378 GLO 0.8795
379 R20 0.8795
380 CMS 0.8794
381 PO6 0.8794
382 XSP 0.8793
383 1X4 0.8792
384 DA4 0.8790
385 PEZ 0.8789
386 MET 0.8789
387 Q9Z 0.8787
388 HSM 0.8787
389 PJL 0.8785
390 HF2 0.8785
391 DPN 0.8784
392 SOL 0.8784
393 CCU 0.8782
394 PIM 0.8779
395 9RW 0.8779
396 URS 0.8778
397 QSC 0.8776
398 FJO 0.8774
399 UN1 0.8774
400 9X7 0.8773
401 RAT 0.8772
402 TZE 0.8771
403 DAR 0.8770
404 FK8 0.8770
405 650 0.8769
406 BTL 0.8769
407 XPO 0.8768
408 K7M 0.8768
409 5AC 0.8768
410 M4T 0.8767
411 8EW 0.8767
412 B40 0.8766
413 54D 0.8763
414 NSD 0.8762
415 KMT 0.8762
416 KIV 0.8761
417 VX 0.8759
418 KDG 0.8758
419 8OZ 0.8757
420 3HP 0.8756
421 SME 0.8753
422 0OC 0.8752
423 0L1 0.8750
424 DER 0.8747
425 L5V 0.8745
426 M58 0.8741
427 JZ5 0.8741
428 I1E 0.8740
429 A8C 0.8740
430 3HG 0.8740
431 S2P 0.8736
432 273 0.8735
433 HCI 0.8733
434 KTA 0.8732
435 1P3 0.8731
436 PEA 0.8728
437 ODV 0.8726
438 DEZ 0.8724
439 HDA 0.8724
440 BNF 0.8723
441 OOG 0.8720
442 MED 0.8716
443 3QM 0.8716
444 NM2 0.8712
445 64Z 0.8709
446 AFS 0.8707
447 CSS 0.8705
448 SSB 0.8697
449 IPU 0.8694
450 4FH 0.8693
451 QDK 0.8691
452 BUB 0.8688
453 J0Z 0.8687
454 C21 0.8686
455 3MB 0.8684
456 NMJ 0.8683
457 PPY 0.8683
458 OHP 0.8678
459 OTR 0.8675
460 264 0.8675
461 O8Y 0.8674
462 PKU 0.8673
463 CXP 0.8669
464 1CO 0.8666
465 MAH 0.8666
466 M45 0.8664
467 8GC 0.8656
468 PRS 0.8656
469 R2P 0.8656
470 SYM 0.8655
471 PEL 0.8655
472 LPK 0.8655
473 FUD 0.8653
474 ARG 0.8651
475 A3M 0.8651
476 2D8 0.8651
477 DHS 0.8650
478 JBN 0.8648
479 ASC 0.8640
480 SC2 0.8639
481 7UC 0.8636
482 SHI 0.8634
483 LY0 0.8634
484 MES 0.8633
485 5HN 0.8631
486 JZ7 0.8631
487 11C 0.8626
488 I38 0.8624
489 7A8 0.8624
490 BRT 0.8623
491 KBB 0.8623
492 BHU 0.8622
493 IT2 0.8619
494 1DU 0.8616
495 HY3 0.8616
496 DBX 0.8609
497 6TZ 0.8603
498 GYE 0.8601
499 HHA 0.8601
500 AC0 0.8600
501 DTT 0.8592
502 268 0.8590
503 XRX 0.8589
504 1KA 0.8583
505 PBA 0.8580
506 GCO 0.8580
507 MRY 0.8578
508 CEE 0.8577
509 TIU 0.8575
510 69O 0.8574
511 PRA 0.8572
512 LNR 0.8570
513 OXQ 0.8563
514 PIY 0.8561
515 GIF 0.8559
516 NYL 0.8554
517 Q02 0.8552
518 WOT 0.8550
519 XXG 0.8547
520 RUY 0.8546
521 GBD 0.8545
522 3MV 0.8527
523 DLT 0.8523
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6JO3; Ligand: 1GP; 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: 6jo3.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6JO3; Ligand: 1GP; 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: 6jo3.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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