Receptor
PDB id Resolution Class Description Source Keywords
3B9G 1.4 Å EC: 3.2.2.1 CRYSTAL STRUCTURE OF LOOP DELETION MUTANT OF TRYPANOSOMA VIV NUCLEOSIDE HYDROLASE (3GTVNH) IN COMPLEX WITH IMMH TRYPANOSOMA VIVAX ROSSMANN FOLD FLEXIBLE LOOP DELETION TRANSITION STATE COMPHYDROLASE
Ref.: A FLEXIBLE LOOP AS A FUNCTIONAL ELEMENT IN THE CATA MECHANISM OF NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA J.BIOL.CHEM. V. 283 22272 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:318;
B:318;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
IMH A:501;
B:502;
Valid;
Valid;
none;
none;
Ki = 19 uM
266.253 C11 H14 N4 O4 c1c(c...
NA A:319;
Part of Protein;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EPW 1.3 Å EC: 3.2.2.1 CRYSTAL STRUCTURE OF TRYPANOSOMA VIVAX NUCLEOSIDE HYDROLASE WITH THE INHIBITOR (2R,3R,4S)-1-[(4-HYDROXY-5H-PYRROLO[3,2-D ]PYRIMIDIN-7-YL)METHYL]-2-(HYDROXYMETHYL)PYRROLIDIN-3,4-DI TRYPANOSOMA VIVAX ROSSMANN FOLD ACTIVE SITE LOOPS AROMATIC STACKING HYDROLA
Ref.: CRYSTAL STRUCTURES OF T. VIVAX NUCLEOSIDE HYDROLASE COMPLEX WITH NEW POTENT AND SPECIFIC INHIBITORS. BIOCHIM.BIOPHYS.ACTA V.1794 953 2009
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3B9G Ki = 19 uM IMH C11 H14 N4 O4 c1c(c2c([n....
2 3EPW Ki = 4.4 nM JMQ C12 H16 N4 O4 c1c(c2c([n....
3 2FF1 Ki = 6.2 nM IMH C11 H14 N4 O4 c1c(c2c([n....
4 1KIC - NOS C10 H12 N4 O5 c1nc2c(n1[....
5 1R4F - AD3 C11 H14 N4 O4 c1cnc(c2c1....
6 1KIE - AD3 C11 H14 N4 O4 c1cnc(c2c1....
7 3EPX Ki = 10.8 nM IMQ C15 H18 N2 O3 c1cc2cccnc....
8 1HP0 Ki = 0.2 uM AD3 C11 H14 N4 O4 c1cnc(c2c1....
9 2FF2 Ki = 6.2 nM IMH C11 H14 N4 O4 c1c(c2c([n....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3B9G Ki = 19 uM IMH C11 H14 N4 O4 c1c(c2c([n....
2 3EPW Ki = 4.4 nM JMQ C12 H16 N4 O4 c1c(c2c([n....
3 2FF1 Ki = 6.2 nM IMH C11 H14 N4 O4 c1c(c2c([n....
4 1KIC - NOS C10 H12 N4 O5 c1nc2c(n1[....
5 1R4F - AD3 C11 H14 N4 O4 c1cnc(c2c1....
6 1KIE - AD3 C11 H14 N4 O4 c1cnc(c2c1....
7 3EPX Ki = 10.8 nM IMQ C15 H18 N2 O3 c1cc2cccnc....
8 1HP0 Ki = 0.2 uM AD3 C11 H14 N4 O4 c1cnc(c2c1....
9 2FF2 Ki = 6.2 nM IMH C11 H14 N4 O4 c1c(c2c([n....
10 4I71 Ki = 18 nM AGV C12 H17 N5 O3 c1c(c2c([n....
11 4I74 - MBY C12 H15 N3 O4 S c1c(c2c(s1....
12 4I73 Ki = 190 nM MBY C12 H15 N3 O4 S c1c(c2c(s1....
13 4I72 Ki = 0.9 nM UA2 C11 H15 N5 O3 c1c(c2c([n....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3B9G Ki = 19 uM IMH C11 H14 N4 O4 c1c(c2c([n....
2 3EPW Ki = 4.4 nM JMQ C12 H16 N4 O4 c1c(c2c([n....
3 2FF1 Ki = 6.2 nM IMH C11 H14 N4 O4 c1c(c2c([n....
4 1KIC - NOS C10 H12 N4 O5 c1nc2c(n1[....
5 1R4F - AD3 C11 H14 N4 O4 c1cnc(c2c1....
6 1KIE - AD3 C11 H14 N4 O4 c1cnc(c2c1....
7 3EPX Ki = 10.8 nM IMQ C15 H18 N2 O3 c1cc2cccnc....
8 1HP0 Ki = 0.2 uM AD3 C11 H14 N4 O4 c1cnc(c2c1....
9 2FF2 Ki = 6.2 nM IMH C11 H14 N4 O4 c1c(c2c([n....
10 4I71 Ki = 18 nM AGV C12 H17 N5 O3 c1c(c2c([n....
11 4I74 - MBY C12 H15 N3 O4 S c1c(c2c(s1....
12 4I73 Ki = 190 nM MBY C12 H15 N3 O4 S c1c(c2c(s1....
13 4I72 Ki = 0.9 nM UA2 C11 H15 N5 O3 c1c(c2c([n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: IMH; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 IMH 1 1
2 UA2 0.645161 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: IMH; Similar ligands found: 437
No: Ligand Similarity coefficient
1 ADN 1.0000
2 9DI 0.9978
3 NOS 0.9969
4 FMC 0.9968
5 TBN 0.9966
6 FMB 0.9963
7 FM1 0.9881
8 XYA 0.9853
9 IMG 0.9826
10 5AD 0.9790
11 GMP 0.9786
12 MTA 0.9771
13 TAL 0.9765
14 MDR 0.9755
15 2FA 0.9750
16 5N5 0.9742
17 MTM 0.9738
18 PRH 0.9733
19 RAB 0.9712
20 1DA 0.9688
21 MTP 0.9688
22 ARJ 0.9687
23 NOC 0.9687
24 MTH 0.9684
25 5ID 0.9683
26 3D1 0.9667
27 NWW 0.9661
28 FM2 0.9643
29 5FD 0.9630
30 HPR 0.9616
31 SNI 0.9613
32 CL9 0.9599
33 A 0.9584
34 A4D 0.9576
35 AD3 0.9568
36 5F1 0.9567
37 FTU 0.9554
38 3AD 0.9547
39 5CD 0.9542
40 6MD 0.9542
41 8OX 0.9536
42 Y3J 0.9509
43 F01 0.9508
44 EKH 0.9507
45 2FD 0.9494
46 4UO 0.9494
47 DBM 0.9489
48 GNG 0.9486
49 6CR 0.9467
50 MTI 0.9459
51 THM 0.9456
52 AFX 0.9450
53 PUR 0.9443
54 5I5 0.9434
55 5UD 0.9420
56 0DN 0.9411
57 MG7 0.9406
58 3BH 0.9403
59 DCF 0.9396
60 CFE 0.9383
61 5NB 0.9377
62 CTN 0.9375
63 5BT 0.9348
64 7D7 0.9331
65 MCY 0.9325
66 URI 0.9320
67 B86 0.9304
68 NWQ 0.9302
69 SCT 0.9297
70 RFZ 0.9283
71 CTD 0.9278
72 5MD 0.9258
73 7CI 0.9255
74 I5A 0.9251
75 DIH 0.9244
76 DNB 0.9242
77 MCF 0.9241
78 CC5 0.9237
79 DUR 0.9233
80 38B 0.9227
81 EP4 0.9226
82 MZR 0.9224
83 N8M 0.9218
84 ID2 0.9216
85 GA2 0.9212
86 Z8B 0.9212
87 8HG 0.9207
88 DCZ 0.9205
89 H7S 0.9204
90 ZJB 0.9199
91 3DT 0.9196
92 3L1 0.9191
93 ZAS 0.9190
94 RPP 0.9186
95 XYS XYP 0.9176
96 SP1 0.9168
97 CDY 0.9162
98 CMP 0.9147
99 XYP XYP 0.9144
100 IM5 0.9140
101 ACE TRP 0.9138
102 26A 0.9136
103 AOC 0.9132
104 MBY 0.9130
105 833 0.9126
106 URD 0.9122
107 ZYV 0.9120
108 JMQ 0.9119
109 TMC 0.9116
110 XYP XYS 0.9105
111 RP1 0.9100
112 TIA 0.9083
113 TR7 0.9082
114 6J3 0.9072
115 KF5 0.9069
116 4GU 0.9065
117 92O 0.9065
118 5AE 0.9063
119 NEC 0.9062
120 XTS 0.9054
121 NEO 0.9053
122 GEO 0.9051
123 THU 0.9047
124 4K2 0.9046
125 TRP 0.9043
126 AGV 0.9041
127 UUA 0.9039
128 TO1 0.9035
129 2QU 0.9030
130 RBV 0.9023
131 CTE 0.9022
132 JA3 0.9021
133 AVX 0.9012
134 HO4 0.9012
135 9UL 0.9008
136 1Q4 0.9007
137 AMP 0.9006
138 X2M 0.9005
139 YE6 0.9004
140 LVY 0.9001
141 3DH 0.8999
142 BMC 0.8997
143 TYU 0.8995
144 JF8 0.8991
145 2TU 0.8991
146 96Z 0.8990
147 F40 0.8985
148 C4E 0.8984
149 LLT 0.8983
150 EAT 0.8978
151 PIR 0.8975
152 XYP XDN 0.8969
153 XDN XYP 0.8968
154 TIZ 0.8966
155 XYP AHR 0.8960
156 13A 0.8956
157 78U 0.8946
158 ZEB 0.8942
159 XYS XYS 0.8940
160 5P7 0.8938
161 DDU 0.8938
162 5ER 0.8937
163 XIF XYP 0.8937
164 P2L 0.8936
165 4CN 0.8931
166 5GV 0.8926
167 2L2 0.8921
168 QQX 0.8920
169 ACK 0.8920
170 2JX 0.8917
171 AR3 0.8916
172 BZM 0.8912
173 6SW 0.8909
174 Q5M 0.8906
175 QQY 0.8902
176 SGP 0.8902
177 35G 0.8901
178 9CE 0.8898
179 1KN 0.8890
180 A4V 0.8890
181 H4B 0.8890
182 WCU 0.8889
183 7CH 0.8889
184 BIO 0.8884
185 7G1 0.8882
186 B5A 0.8878
187 HBI 0.8877
188 EF2 0.8876
189 BVD 0.8875
190 XIL 0.8872
191 DBS 0.8871
192 5JT 0.8869
193 IMQ 0.8867
194 A3N 0.8867
195 PE2 0.8866
196 8DA 0.8864
197 TLF 0.8862
198 22L 0.8862
199 NEU 0.8859
200 NXB 0.8857
201 FT6 0.8856
202 Q9P 0.8854
203 XDL XYP 0.8852
204 C1Y 0.8849
205 6SX 0.8847
206 DHZ 0.8845
207 AOJ 0.8835
208 NQ7 0.8834
209 7GY 0.8832
210 GZV 0.8832
211 MPU 0.8824
212 3D8 0.8822
213 GPK 0.8818
214 WV7 0.8816
215 NE1 0.8815
216 NIY 0.8814
217 ZIQ 0.8813
218 DK4 0.8813
219 XYP XIF 0.8812
220 EXL 0.8810
221 M01 0.8805
222 5V7 0.8805
223 NNR 0.8801
224 FWD 0.8801
225 RVD 0.8798
226 1FL 0.8797
227 2L1 0.8795
228 BRD 0.8792
229 HVE 0.8791
230 RE4 0.8791
231 0OK 0.8790
232 0J4 0.8787
233 3WN 0.8787
234 3WO 0.8787
235 BBY 0.8786
236 UX0 0.8784
237 KWB 0.8782
238 DTE 0.8782
239 KP2 0.8781
240 0GA 0.8781
241 AX8 0.8780
242 IM4 0.8780
243 EXX 0.8778
244 0SY 0.8778
245 AC2 0.8777
246 DNQ 0.8776
247 EXG 0.8775
248 B21 0.8774
249 IMP 0.8773
250 MEX 0.8771
251 JVQ 0.8770
252 SGV 0.8770
253 ITW 0.8769
254 GAL FUC 0.8768
255 A18 0.8768
256 H2B 0.8767
257 1SF 0.8767
258 JO5 0.8765
259 XEV 0.8764
260 BGC GLC 0.8764
261 I0D 0.8764
262 Y70 0.8763
263 D64 0.8761
264 X6P 0.8758
265 CQW 0.8755
266 DBQ 0.8755
267 E1N 0.8755
268 G30 0.8754
269 FCW 0.8752
270 2P3 0.8751
271 DFL 0.8750
272 NAL 0.8749
273 LTN 0.8748
274 3IP 0.8747
275 5E5 0.8746
276 M02 0.8746
277 VCE 0.8745
278 ZEA 0.8744
279 TH4 0.8744
280 DTR 0.8742
281 BC3 0.8741
282 H75 0.8737
283 0OO 0.8736
284 CUT 0.8736
285 3Y7 0.8735
286 BDJ 0.8734
287 CMU 0.8733
288 RNK 0.8733
289 TI7 0.8733
290 AUV 0.8733
291 RR7 GLC 0.8731
292 JY4 0.8731
293 3RP 0.8729
294 88R 0.8728
295 AV4 0.8726
296 NIR 0.8726
297 5NN 0.8724
298 7L4 0.8722
299 QME 0.8722
300 B2L 0.8721
301 B1T 0.8720
302 RVB 0.8720
303 42R 0.8720
304 AZZ 0.8717
305 ALN 0.8716
306 272 0.8715
307 7AP 0.8714
308 OCZ 0.8714
309 3WK 0.8713
310 FY8 0.8713
311 22T 0.8711
312 3AK 0.8707
313 2GQ 0.8702
314 4AB 0.8701
315 5BX 0.8701
316 Q4G 0.8699
317 ZYW 0.8699
318 16Z 0.8698
319 2GD 0.8696
320 0QV 0.8694
321 4L2 0.8690
322 TGW 0.8690
323 EXR 0.8690
324 M0N 0.8689
325 TDI 0.8688
326 QMR 0.8688
327 EQU 0.8684
328 5F7 0.8683
329 II4 0.8683
330 28A 0.8681
331 1ZC 0.8681
332 P4L 0.8680
333 4Z9 0.8680
334 VBC 0.8678
335 DX6 0.8677
336 LL1 0.8677
337 AJ4 0.8676
338 JOB 0.8676
339 092 0.8676
340 EMU 0.8673
341 CUH 0.8672
342 4E5 0.8672
343 5WK 0.8672
344 ANU 0.8669
345 PF1 0.8669
346 DGO Z61 0.8666
347 EV2 0.8665
348 5GP 0.8665
349 5E4 0.8664
350 885 0.8664
351 6ZW 0.8662
352 SCE 0.8660
353 WS6 0.8660
354 C0H 0.8660
355 ZSP 0.8658
356 AGI 0.8655
357 X29 0.8655
358 OLU 0.8653
359 IMK 0.8653
360 BGC GAL 0.8653
361 BGC BMA 0.8652
362 OUA 0.8651
363 Z57 0.8650
364 0FR 0.8649
365 IRP 0.8647
366 DXK 0.8644
367 DA 0.8641
368 QKU 0.8634
369 GPQ 0.8632
370 NAR 0.8632
371 GLC IFM 0.8631
372 CJZ 0.8628
373 KL2 0.8628
374 DAH 0.8628
375 LOX XYP 0.8627
376 WVV 0.8626
377 TMP 0.8621
378 LZJ 0.8620
379 9PP 0.8619
380 W23 0.8618
381 4WF 0.8616
382 BG8 0.8615
383 A4N 0.8614
384 4NR 0.8612
385 N1Y 0.8610
386 M83 0.8609
387 Z15 0.8608
388 FT1 0.8605
389 1VK 0.8603
390 XMM 0.8602
391 6EL 0.8601
392 C2M 0.8601
393 2AM 0.8601
394 ETV 0.8600
395 ZEZ 0.8599
396 SY4 0.8598
397 TCC 0.8597
398 8D6 0.8595
399 RBE 0.8595
400 TH1 0.8594
401 7EH 0.8594
402 EZN 0.8593
403 27M 0.8591
404 848 0.8590
405 TQ3 0.8585
406 5VU 0.8584
407 1YO 0.8583
408 W29 0.8580
409 AS 0.8576
410 51Y 0.8573
411 NWD 0.8572
412 GPU 0.8571
413 YE7 0.8566
414 E9S 0.8565
415 0HY 0.8564
416 Q0K 0.8562
417 BXZ 0.8561
418 2UD 0.8560
419 8OB 0.8556
420 YUG 0.8555
421 KMP 0.8548
422 0UL 0.8539
423 PVQ 0.8538
424 MUK 0.8536
425 A4B 0.8535
426 FUB FUB 0.8534
427 KTM 0.8533
428 GEN 0.8533
429 EDG AHR 0.8532
430 HHV 0.8530
431 RKY 0.8527
432 BMA BMA 0.8522
433 17C 0.8522
434 DI 0.8515
435 LU2 0.8510
436 J84 0.8508
437 D5M 0.8505
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EPW; Ligand: JMQ; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 3epw.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3MKN DNB 33.2278
2 3MKN DNB 33.2278
3 1YOE RIB 38.1988
4 1YOE RIB 38.1988
Pocket No.: 2; Query (leader) PDB : 3EPW; Ligand: JMQ; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 3epw.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3MKN DNB 33.2278
2 3MKN DNB 33.2278
3 1YOE RIB 38.1988
4 1YOE RIB 38.1988
APoc FAQ
Feedback