-->
Receptor
PDB id Resolution Class Description Source Keywords
3PN1 2 Å EC: 6.5.1.2 NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITORS WITH BR SPECTRUM POTENCY AND ANTIBACTERIAL EFFICACY IN VIVO HAEMOPHILUS INFLUENZAE ATP GRASP FOLD LIGASE DNA BACTERIA LIGASE-LIGASE INHIBITCOMPLEX
Ref.: NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITOR BROAD-SPECTRUM ACTIVITY AND ANTIBACTERIAL EFFICACY ANTIMICROB.AGENTS CHEMOTHER. V. 55 1088 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IVH A:319;
Valid;
none;
ic50 = 0.507 uM
355.413 C14 H21 N5 O4 S CCCCS...
IWH A:320;
Invalid;
none;
submit data
256.3 C15 H16 N2 O2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PN1 2 Å EC: 6.5.1.2 NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITORS WITH BR SPECTRUM POTENCY AND ANTIBACTERIAL EFFICACY IN VIVO HAEMOPHILUS INFLUENZAE ATP GRASP FOLD LIGASE DNA BACTERIA LIGASE-LIGASE INHIBITCOMPLEX
Ref.: NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITOR BROAD-SPECTRUM ACTIVITY AND ANTIBACTERIAL EFFICACY ANTIMICROB.AGENTS CHEMOTHER. V. 55 1088 2011
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
2 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
3 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
2 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
3 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1TA8 - NMN C11 H16 N2 O8 P c1cc(c[n+]....
2 4LH7 ic50 = 34 uM 1X8 C9 H8 N4 O2 S c1c2c(c(cn....
3 4LH6 ic50 = 77 uM 1X7 C8 H6 Br N3 O S c1c2c(c(cn....
4 5FPO - 10L C7 H7 N3 c1cc2cn[nH....
5 5FPR - LGA C4 H5 N3 c1cnc(nc1)....
6 4CC6 ic50 = 0.23 uM L5Y C14 H12 F3 N5 O c1cncc2c1c....
7 4CC5 Kd = 38 uM L5V C6 H4 Cl N5 c1c(nc(cn1....
8 4GLW Kd = 0.8 uM 0XT C8 H10 N6 O Cc1c(nc2c(....
9 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
10 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
11 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IVH; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 IVH 1 1
2 2FA 0.567568 0.805195
3 6AD 0.5 0.807229
4 6CR 0.493671 0.794872
5 XYA 0.493333 0.835616
6 RAB 0.493333 0.835616
7 ADN 0.493333 0.835616
8 MTA 0.428571 0.813333
9 MTP 0.419753 0.864865
10 3DH 0.418605 0.837838
11 6MD 0.414634 0.824324
12 26A 0.414634 0.779221
13 1DA 0.414634 0.835616
14 5N5 0.407407 0.810811
15 EO7 0.406593 0.648936
16 EP4 0.404762 0.769231
17 A4D 0.402439 0.835616
18 5CD 0.402439 0.773333
19 DTA 0.4 0.75641
20 M2T 0.4 0.772152
21 DSH 0.4 0.78481
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PN1; Ligand: IVH; Similar sites found with APoc: 481
This union binding pocket(no: 1) in the query (biounit: 3pn1.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4I6H 1C8 0.649351
2 1RE8 BD2 0.943396
3 4WB6 ATP 0.943396
4 4WB7 ATP 0.943396
5 2GU8 796 0.943396
6 1ZP9 ATP 1.16279
7 3AKK ADP 1.25786
8 1KJ8 ATP 1.25786
9 1KJ8 GAR 1.25786
10 5F90 GLA GAL 1.28205
11 5F90 LMR 1.28205
12 5HCY 60D 1.57233
13 5EQY 5RA 1.57233
14 6C1S EFV 1.57233
15 4OH4 ANP 1.57233
16 6BXI ANP 1.57233
17 1Q9I FAD 1.57233
18 1Q9I TEO 1.57233
19 2Q4H AMP 1.57233
20 5YF9 NIO 1.57233
21 2PHN GDP 1.5748
22 3VC1 SAH 1.60256
23 4X7Q 3YR 1.60256
24 5AX9 4KT 1.62338
25 3EKK GS2 1.62866
26 2QQ0 TMP 1.63043
27 2QQ0 ADP 1.63043
28 3BU5 ATP 1.63399
29 6GIN IR2 1.66113
30 1ZX5 LFR 1.66667
31 1PHK ATP 1.67785
32 4WNP 3RJ 1.74216
33 5M06 ADP 1.81159
34 5FBN 5WF 1.84502
35 3DNT ATP 1.88679
36 4N70 2HX 1.88679
37 4BTK DTQ 1.88679
38 3MVH WFE 1.88679
39 3LXN MI1 1.88679
40 3TPV ADE 1.88679
41 4EUU BX7 1.88679
42 4O1P ANP 1.88679
43 1U5R ATP 1.88679
44 3FSY SCA 1.88679
45 5YK1 ANP 1.88679
46 4IE6 UN9 1.88679
47 3FHR P4O 1.88679
48 2F57 23D 1.89274
49 4G6I RS3 1.90476
50 3RE4 TO1 1.93798
51 4NFN 2KC 1.94175
52 4GJ3 0XP 1.98676
53 5WO4 B7V 1.98676
54 4ZGP ADP 2.04778
55 4E1Z 0MX 2.06186
56 1JG3 ADN 2.12766
57 1IA9 ANP 2.14286
58 3VOT ADP 2.20126
59 5C4L 4XR 2.20126
60 5MY8 RXZ 2.20126
61 4UXL 5P8 2.20126
62 2QK4 ATP 2.20126
63 3E7O 35F 2.20126
64 4UX9 ANP 2.20126
65 2WU6 DKI 2.20126
66 5C4L SIS 2.20126
67 3PTG 932 2.20126
68 6FYL 3NG 2.20126
69 2PYW ADP 2.20126
70 1PK8 ATP 2.20126
71 5BO9 SIA GAL NGS 2.20126
72 1V35 NAI 2.20126
73 2PUL ACP 2.20126
74 5VLQ ANP 2.20126
75 1YKD CMP 2.20126
76 1AUX AGS 2.2508
77 4QMN DB8 2.25806
78 6CZ3 FLJ 2.27273
79 1IOW PHY 2.28758
80 1IOW ADP 2.28758
81 5GZ9 ANP 2.29508
82 4I94 ANP 2.33333
83 4AT3 LTI 2.34114
84 1S68 AMP 2.40964
85 5TO8 7FM 2.48227
86 6FL8 ADP 2.51572
87 6FL8 TIY 2.51572
88 5W4W 9WG 2.51572
89 4ASE AV9 2.51572
90 3ALN ANP 2.51572
91 5ERR ADP 2.51572
92 5AE9 OKO 2.51572
93 5C03 AGS 2.51572
94 4KBA 1QM 2.51572
95 5IM3 DTP 2.51572
96 4ONA UW1 2.51572
97 4WNK 453 2.51572
98 1CM8 ANP 2.51572
99 3UDZ ADP 2.51572
100 4WOV 3SM 2.52366
101 4AG8 AXI 2.53165
102 5OKT 9XK 2.54777
103 5K2M ADP 2.5641
104 5JKG 6LF 2.57235
105 2HK5 1BM 2.59259
106 4AUA 4AU 2.60586
107 5NKB 8ZT 2.61438
108 5ZCT ANP 2.61438
109 3TM0 B31 2.6616
110 3TM0 ANP 2.6616
111 6CQF F97 2.6936
112 5VC5 96M 2.76817
113 3VX3 ADP 2.82258
114 4OCV ANP 2.83019
115 3V4S ADP 2.83019
116 4G17 0VN 2.83019
117 5DZT AMP 2.83019
118 3V4S ATP 2.83019
119 4OCJ NDG 2.83019
120 3W0O ADP 2.83019
121 3W0O HY0 2.83019
122 1Q8Y ADE 2.83019
123 3X01 AMP 2.83019
124 4FL3 ANP 2.83019
125 3LXK MI1 2.83019
126 1Q8Y ADP 2.83019
127 4Y0X ADP 2.83019
128 5Y0T TAT 2.83019
129 4P5Z Q7M 2.83019
130 6EZ6 C5Z 2.83019
131 5OES ADP 2.83019
132 2PZI AXX 2.83019
133 4Y93 746 2.83019
134 2Q4W FAD 2.83019
135 5JFS 6K0 2.92208
136 3TDV GDP 2.94118
137 4YMJ 4EJ 2.96053
138 6GUE FB8 2.98507
139 5H2U 1N1 2.99625
140 4U44 3D9 3.01205
141 2BPM 529 3.01887
142 2XMY CDK 3.02013
143 4BCM T7Z 3.05344
144 4BCQ TJF 3.05344
145 4BCN T9N 3.05344
146 4CFU 2WC 3.05344
147 5LMK 6ZK 3.10078
148 3TY5 ADP 3.14465
149 1E4E ADP 3.14465
150 3TY5 ATP 3.14465
151 3HMO STU 3.14465
152 2C29 NAP 3.14465
153 4UWH JXM 3.14465
154 3TKI S25 3.14465
155 1NP7 FAD 3.14465
156 4J7Q B7N 3.14465
157 2HY0 306 3.14465
158 3Q60 ATP 3.14465
159 4U0I 0LI 3.1746
160 1JPA ANP 3.20513
161 1I7L ATP 3.23625
162 3SRV S19 3.2491
163 6CGD GNP 3.27869
164 6CGD AKN 3.27869
165 4USF 6UI 3.28947
166 4F4P 0SB 3.2967
167 4N9I PCG 3.33333
168 5DEY 59T 3.367
169 5XVG 8FX 3.41297
170 5DRB 5FJ 3.43643
171 2JLD AG1 3.45912
172 5EOB 5QQ 3.45912
173 4XH0 ADP 3.45912
174 4JR7 GNP 3.45912
175 2VQD AP2 3.45912
176 5Y86 HRM 3.45912
177 2V7O DRN 3.45912
178 5WNL STU 3.45912
179 4AZW ATP 3.45912
180 4NM5 ADP 3.45912
181 2B9F ADP 3.45912
182 1O9U ADZ 3.45912
183 3F7Z 34O 3.45912
184 3VRY B43 3.45912
185 3TTI KBI 3.45912
186 3WVR AMP 3.45912
187 6GKV SAH 3.45912
188 4UAL 3FV 3.45912
189 1ON3 MCA 3.45912
190 1FP6 ADP 3.46021
191 4YZN 4K5 3.48432
192 4CRL C1I 3.50877
193 3AQV TAK 3.62319
194 4EWH T77 3.63636
195 5JZJ AN2 3.7037
196 3IDB ANP 3.72671
197 2CFM AMP 3.77358
198 2Q7D ANP 3.77358
199 5COU ATP 3.77358
200 4CLI 5P8 3.77358
201 4QTB 38Z 3.77358
202 4E93 GUI 3.77358
203 4PNI KQQ 3.77358
204 4YZC STU 3.77358
205 2V58 LZJ 3.77358
206 5X8I SQZ 3.77358
207 6FYV 3NG 3.77358
208 3VHE 42Q 3.77358
209 6G33 5ID 3.77358
210 4MV1 ADP 3.77358
211 1JGT APC 3.77358
212 1JGT CMA 3.77358
213 5KF9 ACO 3.77358
214 5LPZ ADP 3.77358
215 4L9I 8PR 3.77358
216 5ZTN CUR 3.77358
217 2QCS ANP 3.78007
218 2Y6O 1N1 3.78007
219 5QIN J2V 3.79747
220 2VZ6 FEF 3.83387
221 4EN4 ATP 3.84615
222 4EN4 GT1 3.84615
223 4EN4 GT0 3.84615
224 5UR1 YY9 3.85852
225 5VCV 1N1 3.85852
226 5EH0 5NW 3.87597
227 4R78 AMP 3.8835
228 5ODT ADP 3.88693
229 5A6N U7E 3.88693
230 5LXM ADP 3.88693
231 3VPB ADP 3.90071
232 3VPC ADP 3.90071
233 1IR3 ANP 3.92157
234 4AVV CD 3.92157
235 4AVV GHE 3.92157
236 1PWB GLC GLC 3.9548
237 5IH1 GDP 3.97351
238 5IH1 6BQ 3.97351
239 3GQI ACP 3.9823
240 4C5N ACP 3.98551
241 4C5N PXL 3.98551
242 2VN9 GVD 3.98671
243 5Y80 IRE 4.05405
244 5LPB ADP 4.05405
245 5EW9 5VC 4.05904
246 5U6C 7YS 4.08805
247 2YW2 ATP 4.08805
248 1EHI ADP 4.08805
249 5BVE 4VG 4.08805
250 6GZD LCI 4.08805
251 2IO8 ADP 4.08805
252 2R5T ANP 4.08805
253 4H3Q ANP 4.08805
254 4U98 ACP 4.08805
255 3PP0 03Q 4.08805
256 2B9H ADP 4.08805
257 2B9I ADP 4.08805
258 4CYI ATP 4.08805
259 5OMY 9YE 4.08805
260 2PVN P63 4.08805
261 3KLL MAL 4.08805
262 6ES0 BW8 4.10095
263 3E5A VX6 4.10448
264 5HVJ ANP 4.12698
265 5USZ SKE 4.15225
266 5L8L ADP 4.2735
267 4IX4 ADP 4.28571
268 2XVD AS6 4.30464
269 3GC0 AMP 4.40252
270 5UIU 8CG 4.40252
271 1WVG CXY 4.40252
272 4PQG UDP 4.40252
273 2PVF ACP 4.40252
274 4TWP AXI 4.42804
275 3CY2 MB9 4.4586
276 5C1P DAL DAL 4.57516
277 5C1P ADP 4.57516
278 2PK3 GDD 4.6729
279 1MEX RAC 4.69484
280 1CKN GTP 4.71698
281 1CKM GTP 4.71698
282 2XK9 XK9 4.71698
283 4OAV ACP 4.71698
284 5UAV NDP 4.71698
285 5UAV TFB 4.71698
286 4F9C 0SX 4.71698
287 3KN5 ANP 4.71698
288 2I0K FAD 4.71698
289 6F3G CJN 4.74576
290 6GWR FEW 4.7619
291 4O4F ATP 4.83871
292 4O4F IHP 4.83871
293 1U7Z PMT 4.86726
294 4RDL FUC GAL NDG FUC 4.87013
295 4L3L 5FI 4.93421
296 2XOC ADP 4.98084
297 3GGF GVD 4.98339
298 3DLS ADP 5.03145
299 6C0T EE4 5.03145
300 1QM5 GLC GLC GLC PO4 SGC GLC 5.03145
301 6BFN DL1 5.03145
302 5Y0N ATP 5.03145
303 3FWN ATR 5.03145
304 3FWN 6PG 5.03145
305 1BYG STU 5.03597
306 3N1S 5GP 5.04202
307 2OFV 242 5.05415
308 4AU8 Z3R 5.06757
309 5EYK 5U5 5.08475
310 3RI1 3RH 5.11182
311 3O0G 3O0 5.13699
312 1UNH IXM 5.13699
313 2WQN ADP 5.16129
314 3FW3 GLC 5.26316
315 5IGI GMP 5.31561
316 5IGI ZIT 5.31561
317 3UIM ANP 5.34591
318 6CMJ F6J 5.34591
319 3KRL KRL 5.34591
320 4IZY 1J2 5.34591
321 1XDN ATP 5.41516
322 4XBA 5GP 5.5
323 4IEN GDP 5.52147
324 5MW8 ATP 5.66038
325 5AWM ANP 5.66038
326 5TDF ADP 5.66038
327 5T8O 76Z 5.66038
328 1Y57 MPZ 5.66038
329 2H8H H8H 5.66038
330 4WHZ 3NL 5.66038
331 3WO0 ALA 5.66038
332 3WO0 ADP 5.66038
333 5DXT 5H5 5.66038
334 5FI4 5XV 5.66038
335 5WS9 AMP 5.66038
336 3IGO ANP 5.66038
337 3K5I ADP 5.66038
338 3K5I AIR 5.66038
339 5DBX ANP 5.66038
340 5DNK SAH 5.66038
341 5CEO 50D 5.66667
342 3HAV ATP 5.68562
343 1GSA ADP 5.6962
344 3PLS ANP 5.7047
345 4A4X JUP 5.73477
346 1V0O INR 5.90278
347 4NZN ANP 5.97484
348 4NZN 2OU 5.97484
349 3GC8 B45 5.97484
350 4IDT T28 5.97484
351 4LOO SB4 5.97484
352 5EKO N17 5.97484
353 5JAQ NAI 5.97484
354 6C7Y ADP 5.98291
355 1K3A ACP 6.02007
356 5LVP ATP 6.10932
357 3DAK ANP 6.2069
358 4CQB MLI 6.28931
359 3C0G 3AM 6.28931
360 2QX0 PH2 6.28931
361 3G5D 1N1 6.29371
362 5TT6 ATP 6.60377
363 2VPQ ANP 6.60377
364 4K38 SAM 6.60377
365 3ND6 ATP 6.60377
366 6GBC AMP 6.60377
367 4K39 SAM 6.60377
368 4K37 SAM 6.60377
369 3I0O ADP 6.60377
370 5FVJ ACO 6.62651
371 3KAL ADP 6.91824
372 4OTH DRN 6.91824
373 4DFU QUE 6.91824
374 3HZT J60 6.91824
375 4KRI SAH 6.91824
376 4IJP 1EH 6.91824
377 1TMM HHR 6.96203
378 1TMM APC 6.96203
379 3KMW ATP 6.97674
380 5A89 ADP 7.05128
381 5A89 FMN 7.05128
382 4LRJ ANP 7.10059
383 3FHI ANP 7.14286
384 2GQS ADP 7.173
385 2GQR ADP 7.173
386 4PZ6 GMP 7.2327
387 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 7.2327
388 2JDR L20 7.2327
389 3ETH ATP 7.2327
390 1VLJ NAP 7.2327
391 4XYM A12 7.3913
392 4XZ3 ACP 7.3913
393 4RFM 3P6 7.5188
394 6AC9 ANP 7.54717
395 4BFM ANP 7.54717
396 3M2W L8I 7.69231
397 5HES 032 7.81759
398 4NJH 2K8 7.82609
399 4NJH SAM 7.82609
400 3GNI ATP 7.86164
401 3ORK AGS 8.03859
402 4WW7 AMP 8.04598
403 4M69 ANP 8.12721
404 5TA6 79D 8.1761
405 3FC2 IBI 8.1761
406 3E8N VRA 8.1761
407 3E8N ATP 8.1761
408 4GYI ADP 8.1761
409 3VSV XYS 8.1761
410 2HGS ADP 8.1761
411 3VPD ANP 8.18505
412 5XG5 A2G 8.27586
413 2BKK ADP 8.28402
414 6A1G 9OL 8.49057
415 2Z7R STU 8.49057
416 5ZQS XYP 8.49057
417 4BHN BH9 8.49057
418 3TII ANP 8.49057
419 2F2U M77 8.49057
420 3SLS ANP 8.55263
421 2CSN CKI 8.75421
422 3V8S 0HD 8.80503
423 3TXO 07U 9.1195
424 6E2O S0L 9.15254
425 4Y8D 49J 9.28571
426 1U59 STU 9.40767
427 4NW6 2NS 9.43396
428 5VZ0 ADP 9.43396
429 6FKW PQQ 9.43396
430 6GU6 1QK 9.52381
431 5HQ0 LZ9 9.52381
432 3QKT ANP 9.74843
433 4NAT 2W5 10
434 1ST0 GTG 10.3774
435 2IF8 ADP 10.3774
436 6G34 5ID 10.6918
437 4OUC 5ID 10.6918
438 1ZY5 ANP 10.8911
439 5I35 ANP 11.0063
440 3H9R TAK 11.0092
441 5G1X ADP 11.1111
442 5UKL SIX 11.2903
443 1Z2P ACP 11.3208
444 1Z2P I3S 11.3208
445 1T36 ADP 11.3208
446 5DH3 5BS 11.4286
447 4Z4P SAH 11.4458
448 4C2W ANP 11.5385
449 2R7K ACP 11.6352
450 2R7K AMZ 11.6352
451 4FG8 ATP 11.746
452 4PU5 ANP 11.9497
453 4XV1 904 11.9863
454 5UPK ANP 12.5
455 4ZS4 ATP 13.0293
456 1W2D 4IP 13.5849
457 1W2D ADP 13.5849
458 3SXS PP2 13.806
459 3ORQ ADP 13.8365
460 2QF7 AGS 13.8365
461 1M0W ANP 14.1509
462 4NFE BEN 14.346
463 3PDT ADP 14.5455
464 4NST ADP 14.5522
465 5EFQ ADP 14.5522
466 5LI1 ANP 15
467 3C1X CKK 15.0943
468 1XJD STU 15.0943
469 2A19 ANP 15.1408
470 5LXT ACP 16.3522
471 4CSV STI 17.0909
472 4Q5H ANP 17.1053
473 4FE2 ADP 17.2549
474 2YAK OSV 17.5439
475 2YAB AMP 18.239
476 5O1I 9GH 18.7215
477 1F2U ATP 20.9459
478 3ZRM ZRM 25
479 4H3P ANP 29.1667
480 4DC2 ADE 35.7143
481 2B9J ADP 38.4615
APoc FAQ
Feedback