Receptor
PDB id Resolution Class Description Source Keywords
2R8Q 1.5 Å EC: 3.1.4.17 STRUCTURE OF LMJPDEB1 IN COMPLEX WITH IBMX LEISHMANIA MAJOR LEISHIMANIASIS PARASITE INHIBITOR SELECTIVITY CAMP PHOSPHODIESTERASE HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE LEISHMANIA MAJOR PHOSPHODIESTERASE LMJPDEB1 AND INSIGHT INTO THE DESIGN OF THE PARASITE-SELECTIVE INHIBITORS. MOL.MICROBIOL. V. 66 1029 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IBM A:3;
B:3;
Valid;
Valid;
none;
none;
ic50 = 580 uM
222.244 C10 H14 N4 O2 CC(C)...
MG A:2;
B:2;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
ZN A:1;
B:1;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2R8Q 1.5 Å EC: 3.1.4.17 STRUCTURE OF LMJPDEB1 IN COMPLEX WITH IBMX LEISHMANIA MAJOR LEISHIMANIASIS PARASITE INHIBITOR SELECTIVITY CAMP PHOSPHODIESTERASE HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE LEISHMANIA MAJOR PHOSPHODIESTERASE LMJPDEB1 AND INSIGHT INTO THE DESIGN OF THE PARASITE-SELECTIVE INHIBITORS. MOL.MICROBIOL. V. 66 1029 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 2R8Q ic50 = 580 uM IBM C10 H14 N4 O2 CC(C)CN1c2....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5G2B Ki = 0.1 uM LQY C31 H36 N4 O4 COc1ccc(cc....
2 5L8Y Ki = 400 nM CVA C33 H40 N4 O5 COc1ccc(cc....
3 5G5V Ki = 200 nM 8Z4 C29 H33 N3 O4 CC(C)N1C(=....
4 6RB6 - JX2 C30 H33 N3 O4 COc1ccc(cc....
5 5G57 Ki = 4 nM 6M5 C33 H40 N6 O4 COc1ccc(cc....
6 5L8C Ki = 100 nM 908 C27 H30 N4 O4 CC(C)N1C(=....
7 6RGK - K3N C29 H39 N3 O3 CCCCNC(=O)....
8 6RFN Ki = 0.00000079 M K3W C28 H29 N3 O4 CC(C)N1C(=....
9 6RFW Ki = 0.00000079 M K1Q C29 H30 F N3 O3 CC(C)N1C(=....
10 5L9H ic50 = 0.4 uM CVL C26 H32 N6 O4 CC(C)N1C(=....
11 6GXQ Ki = 0.00000079 M FFZ C28 H29 N3 O3 CC(C)N1C(=....
12 2R8Q ic50 = 580 uM IBM C10 H14 N4 O2 CC(C)CN1c2....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 5G2B Ki = 0.1 uM LQY C31 H36 N4 O4 COc1ccc(cc....
2 5L8Y Ki = 400 nM CVA C33 H40 N4 O5 COc1ccc(cc....
3 5G5V Ki = 200 nM 8Z4 C29 H33 N3 O4 CC(C)N1C(=....
4 6RB6 - JX2 C30 H33 N3 O4 COc1ccc(cc....
5 5G57 Ki = 4 nM 6M5 C33 H40 N6 O4 COc1ccc(cc....
6 5L8C Ki = 100 nM 908 C27 H30 N4 O4 CC(C)N1C(=....
7 6RGK - K3N C29 H39 N3 O3 CCCCNC(=O)....
8 6RFN Ki = 0.00000079 M K3W C28 H29 N3 O4 CC(C)N1C(=....
9 6RFW Ki = 0.00000079 M K1Q C29 H30 F N3 O3 CC(C)N1C(=....
10 5L9H ic50 = 0.4 uM CVL C26 H32 N6 O4 CC(C)N1C(=....
11 6GXQ Ki = 0.00000079 M FFZ C28 H29 N3 O3 CC(C)N1C(=....
12 2R8Q ic50 = 580 uM IBM C10 H14 N4 O2 CC(C)CN1c2....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: IBM; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 IBM 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: IBM; Similar ligands found: 618
No: Ligand Similarity coefficient
1 5OF 0.9522
2 FXH 0.9472
3 T6Z 0.9465
4 NTZ 0.9456
5 57O 0.9438
6 4KL 0.9356
7 QMS 0.9345
8 S3B 0.9344
9 JR2 0.9342
10 NLA 0.9342
11 MVL 0.9318
12 5WU 0.9312
13 PVK 0.9304
14 OUB 0.9304
15 NBG 0.9304
16 PVQ 0.9299
17 F5C 0.9295
18 9GP 0.9272
19 M3Q 0.9264
20 8XQ 0.9263
21 CPW 0.9260
22 DNC 0.9260
23 GIM 0.9255
24 AIN 0.9253
25 CGW 0.9249
26 KED 0.9248
27 F95 0.9243
28 HTP 0.9240
29 KGK 0.9230
30 L7T 0.9228
31 LIP 0.9228
32 GT0 0.9223
33 AEZ 0.9219
34 PFB 0.9218
35 LZ2 0.9215
36 M3S 0.9210
37 226 0.9208
38 5NS 0.9204
39 QM1 0.9203
40 I4D 0.9201
41 8GK 0.9180
42 790 0.9177
43 9KH 0.9172
44 6DP 0.9169
45 S7B 0.9162
46 LI6 0.9154
47 3N4 0.9153
48 XFE 0.9152
49 5WY 0.9152
50 FLV 0.9147
51 W8G 0.9147
52 CR1 0.9144
53 9KT 0.9142
54 YO5 0.9141
55 7B3 0.9141
56 ZZ8 0.9141
57 HNQ 0.9138
58 3Y7 0.9137
59 BA5 0.9128
60 TTY 0.9123
61 12B 0.9116
62 9FQ 0.9108
63 K3Q 0.9108
64 5NE 0.9106
65 EYA 0.9105
66 2ZQ 0.9104
67 BK9 0.9102
68 DPZ 0.9097
69 X8D 0.9095
70 ONZ 0.9093
71 MIG 0.9090
72 DNA 0.9089
73 4AN 0.9087
74 ARP 0.9083
75 537 0.9078
76 7ZE 0.9077
77 64E 0.9077
78 C9E 0.9077
79 OA3 0.9071
80 EYM 0.9071
81 GOX 0.9069
82 CG8 0.9067
83 GTV 0.9067
84 UQ1 0.9066
85 CKU 0.9066
86 KYA 0.9065
87 8WZ 0.9064
88 L21 0.9063
89 E7R 0.9059
90 6VD 0.9059
91 209 0.9059
92 NCV 0.9057
93 6HP 0.9057
94 NBV 0.9056
95 YKG 0.9053
96 64C 0.9052
97 UFO 0.9051
98 HPT 0.9050
99 I59 0.9048
100 G1P 0.9048
101 KLK 0.9048
102 SRO 0.9045
103 MT8 0.9045
104 2K8 0.9043
105 28S 0.9040
106 NAG 0.9040
107 HHT 0.9036
108 64F 0.9036
109 JXZ 0.9035
110 B56 0.9035
111 MAG 0.9035
112 NPA 0.9032
113 4ME 0.9032
114 KJ5 0.9030
115 6BL 0.9030
116 ALN 0.9030
117 P9T 0.9030
118 K2P 0.9029
119 7WR 0.9028
120 TNF 0.9025
121 CBF 0.9025
122 680 0.9024
123 H33 0.9023
124 MHK 0.9022
125 KFH 0.9021
126 ZVO 0.9020
127 AC2 0.9020
128 TNL 0.9018
129 GRX 0.9017
130 06B 0.9017
131 G6P 0.9014
132 CIP 0.9009
133 7FF 0.9007
134 GDL 0.9007
135 5WX 0.9005
136 SYR 0.9005
137 2CZ 0.9003
138 3RI 0.9003
139 BGC 0.9002
140 APS 0.9001
141 IAC 0.9000
142 LDR 0.9000
143 3GQ 0.9000
144 BDP 0.8998
145 3MG 0.8996
146 EVA 0.8996
147 GP1 0.8995
148 NDG 0.8995
149 E1K 0.8994
150 96R 0.8994
151 7I2 0.8991
152 QPR 0.8991
153 CCV 0.8989
154 PYQ 0.8988
155 IBC 0.8985
156 15L 0.8984
157 GLC 0.8984
158 7SX 0.8984
159 MXX 0.8983
160 IPD 0.8983
161 8S0 0.8980
162 GCB 0.8979
163 PRZ 0.8978
164 JKZ 0.8978
165 9AP 0.8976
166 9UG 0.8975
167 H5B 0.8974
168 L8J 0.8974
169 GTZ 0.8973
170 JYT 0.8973
171 7ZC 0.8972
172 B60 0.8970
173 18N 0.8970
174 8VE 0.8968
175 F34 0.8968
176 GCU 0.8966
177 512 0.8965
178 3GC 0.8965
179 TQU 0.8960
180 5V7 0.8959
181 FA6 0.8953
182 GOG 0.8951
183 FBG 0.8951
184 M0Q 0.8950
185 JXW 0.8950
186 JV4 0.8949
187 O2A 0.8947
188 NID 0.8947
189 LGC 0.8947
190 28N 0.8946
191 GFP 0.8946
192 61M 0.8945
193 RH1 0.8944
194 A1Y 0.8943
195 APZ 0.8942
196 G3F 0.8941
197 KIB 0.8940
198 MQB 0.8940
199 IPT 0.8939
200 PXL 0.8938
201 CFF 0.8938
202 7CT 0.8935
203 TSR 0.8935
204 2KA 0.8934
205 49N 0.8932
206 60Q 0.8931
207 67Y 0.8930
208 SR4 0.8929
209 MYI 0.8929
210 BY5 0.8929
211 H7Y 0.8927
212 3C1 0.8927
213 KIF 0.8926
214 I6G 0.8925
215 TIY 0.8924
216 UQ 0.8922
217 BNT 0.8922
218 8HC 0.8921
219 YSO 0.8920
220 H05 0.8920
221 3B4 0.8919
222 M4B 0.8917
223 GAL 0.8917
224 VK3 0.8917
225 2SX 0.8917
226 XM5 0.8916
227 KBG 0.8915
228 LOG 0.8914
229 2JK 0.8913
230 GCS 0.8913
231 SHG 0.8913
232 67X 0.8911
233 NDM 0.8911
234 VYM 0.8911
235 JXK 0.8911
236 LTM 0.8909
237 15A 0.8909
238 UAN 0.8908
239 96U 0.8906
240 RXA 0.8906
241 ALR 0.8905
242 M0W 0.8903
243 1X8 0.8901
244 EOL 0.8898
245 HQD 0.8895
246 30G 0.8894
247 TRF 0.8892
248 XJE 0.8892
249 GC2 0.8888
250 K68 0.8888
251 MAQ 0.8885
252 GO0 0.8883
253 THA 0.8882
254 772 0.8882
255 PEY 0.8881
256 FSU 0.8880
257 X04 0.8879
258 NQH 0.8879
259 CKA 0.8878
260 M02 0.8878
261 SYA 0.8877
262 C2Y 0.8877
263 5PX 0.8876
264 O2Y 0.8876
265 XQK 0.8875
266 EXL 0.8875
267 4XV 0.8875
268 EJZ 0.8874
269 8MO 0.8874
270 GSY 0.8870
271 NQ 0.8869
272 61O 0.8869
273 3C2 0.8868
274 TEP 0.8867
275 GPM 0.8866
276 BB4 0.8866
277 7VS 0.8866
278 3Z8 0.8865
279 774 0.8864
280 PH2 0.8861
281 JUG 0.8859
282 3J8 0.8858
283 HJB 0.8858
284 SNG 0.8856
285 9F8 0.8855
286 0FK 0.8855
287 AP4 0.8855
288 54X 0.8854
289 G1O 0.8853
290 0N7 0.8851
291 ZYR 0.8851
292 EY7 0.8851
293 JUO 0.8850
294 NVU 0.8849
295 582 0.8849
296 MBG 0.8848
297 7M6 0.8847
298 MT5 0.8846
299 2LY 0.8845
300 GL1 0.8840
301 PLP 0.8839
302 DBJ 0.8838
303 2J9 0.8838
304 NGO 0.8838
305 DK1 0.8838
306 AA 0.8838
307 UXH 0.8838
308 HLZ 0.8837
309 GV9 0.8837
310 2D3 0.8833
311 H6B 0.8832
312 9PY 0.8831
313 HHR 0.8831
314 4XS 0.8830
315 JYK 0.8830
316 AM1 0.8829
317 4MX 0.8829
318 UEG 0.8826
319 4MU 0.8826
320 5RO 0.8826
321 GYP 0.8826
322 D07 0.8826
323 11G 0.8826
324 AZ9 0.8822
325 JTH 0.8820
326 2KU 0.8820
327 2MN 0.8818
328 4B0 0.8816
329 VC2 0.8816
330 44V 0.8812
331 F6P 0.8812
332 GI3 0.8811
333 6J9 0.8810
334 ST1 0.8805
335 IOS 0.8803
336 ANF 0.8803
337 PRF 0.8803
338 PE0 0.8802
339 TSS 0.8800
340 S3C 0.8800
341 TWB 0.8798
342 M5N 0.8798
343 2FQ 0.8797
344 QZ8 0.8796
345 FDR 0.8795
346 6ME 0.8795
347 M1H 0.8793
348 N8Y 0.8793
349 MQG 0.8792
350 F12 0.8791
351 091 0.8791
352 GLS 0.8787
353 ZON 0.8787
354 AO6 0.8786
355 C2U 0.8785
356 2LB 0.8784
357 1X7 0.8783
358 AQO 0.8781
359 JP2 0.8779
360 GLG 0.8779
361 Q6T 0.8777
362 HLD 0.8776
363 PXP 0.8775
364 B62 0.8775
365 NGT 0.8774
366 JAK 0.8773
367 KFN 0.8773
368 FDB 0.8773
369 CLZ 0.8771
370 BG6 0.8771
371 1QP 0.8769
372 505 0.8769
373 GDE 0.8769
374 2L3 0.8768
375 9BF 0.8768
376 PHH 0.8767
377 INE 0.8767
378 S0G 0.8766
379 MEW 0.8766
380 BM3 0.8763
381 AZ8 0.8763
382 4XY 0.8762
383 BRV 0.8762
384 LP8 0.8761
385 XHP 0.8761
386 M5K 0.8761
387 FOT 0.8761
388 MOK 0.8760
389 FWB 0.8759
390 GL4 0.8759
391 42C 0.8758
392 MM2 0.8757
393 SBK 0.8757
394 0LH 0.8757
395 2CL 0.8756
396 NTM 0.8756
397 25O 0.8755
398 3IT 0.8755
399 4HC 0.8755
400 5JT 0.8755
401 F52 0.8755
402 ZZZ 0.8755
403 JY2 0.8754
404 JYW 0.8752
405 LZB 0.8751
406 MIF 0.8750
407 68A 0.8749
408 DNF 0.8748
409 TWO 0.8747
410 TRP 0.8747
411 5VJ 0.8745
412 AKH 0.8745
413 8W9 0.8745
414 JXN 0.8745
415 Z5P 0.8744
416 44W 0.8743
417 JF2 0.8742
418 B57 0.8740
419 AJ2 0.8740
420 1FF 0.8740
421 KG1 0.8740
422 AY4 0.8739
423 GI1 0.8739
424 EMZ 0.8735
425 2F8 0.8733
426 DBQ 0.8732
427 OMD 0.8731
428 2EC 0.8731
429 HHS 0.8729
430 VXX 0.8729
431 1SS 0.8729
432 KJY 0.8728
433 37T 0.8728
434 JF1 0.8726
435 QX4 0.8726
436 VNL 0.8726
437 RVE 0.8724
438 HJP 0.8721
439 L1Q 0.8721
440 BPU 0.8721
441 IJZ 0.8721
442 OSB 0.8720
443 TVP 0.8720
444 GHM 0.8720
445 I3C 0.8720
446 92P 0.8718
447 Q5M 0.8717
448 HBO 0.8717
449 NGA 0.8717
450 KTW 0.8716
451 ASE 0.8714
452 MNS 0.8712
453 AKD 0.8711
454 LT8 0.8711
455 K32 0.8711
456 MMA 0.8710
457 KIA 0.8708
458 DQU 0.8708
459 HWH 0.8707
460 P84 0.8704
461 9UL 0.8702
462 QQQ 0.8702
463 5RN 0.8701
464 49O 0.8699
465 CTE 0.8698
466 6XI 0.8696
467 ZYV 0.8696
468 MAN 0.8695
469 R6T 0.8694
470 IBF 0.8692
471 HKD 0.8692
472 F69 0.8691
473 1HN 0.8690
474 1U7 0.8686
475 FA3 0.8683
476 BMA 0.8683
477 PX7 0.8683
478 EXR 0.8683
479 9LI 0.8683
480 7NI 0.8682
481 HA7 0.8680
482 CLU 0.8679
483 PQ0 0.8679
484 7ME 0.8679
485 DTE 0.8679
486 948 0.8678
487 V55 0.8678
488 4RU 0.8677
489 0P6 0.8676
490 E35 0.8675
491 GNV 0.8674
492 BNX 0.8672
493 7VJ 0.8671
494 JU2 0.8669
495 4TU 0.8669
496 4OG 0.8665
497 1U6 0.8665
498 GTL 0.8664
499 PXM 0.8664
500 PMP 0.8661
501 AMG 0.8661
502 TOF 0.8660
503 XH2 0.8660
504 FUJ 0.8658
505 B4O 0.8657
506 RB2 0.8657
507 M6P 0.8657
508 LSA 0.8657
509 465 0.8655
510 BZM 0.8655
511 MO8 0.8655
512 MUR 0.8654
513 IOP 0.8652
514 ZME 0.8650
515 DIU 0.8650
516 MM1 0.8649
517 15N 0.8648
518 GTR 0.8645
519 CMU 0.8642
520 DTR 0.8642
521 SG2 0.8640
522 NPL 0.8640
523 NIP 0.8639
524 3C4 0.8639
525 DQA 0.8639
526 M1P 0.8638
527 878 0.8638
528 2H5 0.8638
529 0F9 0.8636
530 BPS 0.8636
531 DHK 0.8636
532 S0I 0.8636
533 EGR 0.8635
534 M1E 0.8635
535 8DA 0.8635
536 CSN 0.8635
537 7MX 0.8634
538 149 0.8633
539 8WT 0.8632
540 V1T 0.8632
541 DEE 0.8632
542 KDO 0.8632
543 QNA 0.8630
544 S8A 0.8629
545 OTD 0.8628
546 22L 0.8626
547 2AN 0.8625
548 SBI 0.8624
549 M2K 0.8622
550 A0O 0.8621
551 DQN 0.8619
552 78P 0.8619
553 B52 0.8617
554 P0P 0.8616
555 MNP 0.8616
556 ML1 0.8614
557 K37 0.8611
558 MXD 0.8610
559 LAO 0.8610
560 S3P 0.8608
561 GIV 0.8606
562 9MG 0.8606
563 ONR 0.8605
564 KP6 0.8605
565 G12 0.8603
566 KDM 0.8601
567 GLA 0.8599
568 2FG 0.8598
569 HA5 0.8597
570 FUZ 0.8596
571 4NO 0.8595
572 89J 0.8595
573 K17 0.8590
574 TBS 0.8590
575 55D 0.8588
576 FE DB1 0.8587
577 UFV 0.8584
578 QSH 0.8583
579 Q7A 0.8577
580 A2G 0.8575
581 KP2 0.8574
582 N7I 0.8570
583 39A 0.8570
584 4WF 0.8570
585 8NX 0.8569
586 CKX 0.8567
587 GNJ 0.8566
588 SXS 0.8562
589 PQZ 0.8562
590 PYU 0.8561
591 1Z8 0.8560
592 YIO 0.8560
593 GCV 0.8555
594 K25 0.8554
595 9X5 0.8553
596 SFU 0.8552
597 HMD 0.8551
598 JAA 0.8549
599 MM5 0.8548
600 DY5 0.8547
601 ALL 0.8546
602 M4E 0.8546
603 F1A 0.8545
604 1GN 0.8545
605 3LJ 0.8544
606 23J 0.8540
607 RPQ 0.8537
608 692 0.8536
609 0W8 0.8536
610 HZQ 0.8530
611 Q77 0.8523
612 ADA 0.8523
613 ZB1 0.8521
614 39U 0.8520
615 MCO 0.8517
616 6R8 0.8517
617 DHY 0.8512
618 HBI 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2R8Q; Ligand: IBM; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 2r8q.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5OHJ 9VE 44.8468
Pocket No.: 2; Query (leader) PDB : 2R8Q; Ligand: IBM; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 2r8q.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5OHJ 9VE 44.8468
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