Receptor
PDB id Resolution Class Description Source Keywords
5FPR 2 Å EC: 6.5.1.2 STRUCTURE OF BACTERIAL DNA LIGASE WITH SMALL-MOLECULE LIGAND PYRIMIDIN-2-AMINE (AT371) IN AN ALTERNATE BINDING S ITE. STAPHYLOCOCCUS AUREUS LIGASE ANTIBIOTIC DESIGN PROTEIN-LIGAND COMPLEX FRAGMENT SCREENING ALTERNATE BINDING SITE AT371.
Ref.: DETECTION OF SECONDARY BINDING SITES IN PROTEINS US FRAGMENT SCREENING. PROC.NATL.ACAD.SCI.USA V. 112 15910 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1311;
A:1310;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
LGA A:1312;
Valid;
none;
submit data
95.103 C4 H5 N3 c1cnc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CC6 2.01 Å EC: 6.5.1.2 FRAGMENT-BASED DISCOVERY OF 6 AZAINDAZOLES AS INHIBITORS OF BACTERIAL DNA LIGASE STAPHYLOCOCCUS AUREUS LIGASE LIGA ANTIBIOTIC DESIGN
Ref.: FRAGMENT-BASED DISCOVERY OF 6-AZAINDAZOLES AS INHIB BACTERIAL DNA LIGASE. ACS MED.CHEM.LETT. V. 4 1208 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FPO - 10L C7 H7 N3 c1cc2cn[nH....
2 5FPR - LGA C4 H5 N3 c1cnc(nc1)....
3 4CC6 ic50 = 0.23 uM L5Y C14 H12 F3 N5 O c1cncc2c1c....
4 4CC5 Kd = 38 uM L5V C6 H4 Cl N5 c1c(nc(cn1....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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(....
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 Ki = 110 nM 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 (2D)
Ligand no: 1; Ligand: LGA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LGA 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: LGA; Similar ligands found: 566
No: Ligand Similarity coefficient
1 3AP 1.0000
2 HAI 1.0000
3 CXL 1.0000
4 CYH 1.0000
5 7EX 1.0000
6 V1L 1.0000
7 A2Q 1.0000
8 WOT 1.0000
9 MBN 1.0000
10 HRZ 1.0000
11 IPH 1.0000
12 HVK 1.0000
13 4AP 1.0000
14 9PO 1.0000
15 2AP 1.0000
16 8CL 0.9966
17 2IM 0.9965
18 GXE 0.9925
19 HHN 0.9916
20 TTO 0.9885
21 L60 0.9880
22 93B 0.9840
23 HGW 0.9827
24 PIH 0.9824
25 BAQ 0.9808
26 MZ0 0.9801
27 1CB 0.9793
28 HSL 0.9792
29 3MT 0.9787
30 5MP 0.9778
31 3TR 0.9775
32 2MZ 0.9774
33 4MZ 0.9762
34 MR3 0.9759
35 MZY 0.9750
36 282 0.9747
37 AMT 0.9747
38 GBL 0.9740
39 HOW 0.9739
40 2AI 0.9727
41 1MZ 0.9727
42 DUC 0.9722
43 4XX 0.9712
44 MB3 0.9710
45 HYN 0.9692
46 5KX 0.9690
47 HPY 0.9688
48 CYT 0.9683
49 JZ6 0.9677
50 DGY 0.9676
51 KSW 0.9673
52 LG3 0.9673
53 ECE 0.9666
54 URA 0.9660
55 PCR 0.9658
56 B20 0.9656
57 MMZ 0.9655
58 4JU 0.9655
59 ATQ 0.9654
60 CEJ 0.9654
61 BYZ 0.9650
62 BNZ 0.9644
63 3ZQ 0.9642
64 3ZS 0.9634
65 ES3 0.9633
66 RCO 0.9631
67 26D 0.9630
68 HQE 0.9628
69 XIX 0.9627
70 0PY 0.9625
71 93Q 0.9623
72 LG4 0.9622
73 DMI 0.9621
74 CRS 0.9619
75 FPI 0.9615
76 NVI 0.9613
77 8LG 0.9612
78 P1R 0.9606
79 HBX 0.9603
80 2KT 0.9601
81 NBE 0.9601
82 PHZ 0.9600
83 LG5 0.9600
84 8GF 0.9599
85 PYF 0.9595
86 PLQ 0.9592
87 DTI 0.9590
88 4AX 0.9590
89 24T 0.9589
90 CAQ 0.9588
91 DA1 0.9583
92 25R 0.9583
93 3CH 0.9583
94 PXY 0.9581
95 1AN 0.9580
96 25T 0.9578
97 SYN 0.9578
98 BEW 0.9576
99 BVF 0.9575
100 PYZ 0.9574
101 FP2 0.9572
102 2MH 0.9562
103 FPN 0.9553
104 284 0.9550
105 JZ0 0.9549
106 ABN 0.9547
107 92Z 0.9544
108 AMC 0.9543
109 PY7 0.9542
110 HIU 0.9540
111 E60 0.9537
112 280 0.9536
113 938 0.9533
114 OXL 0.9528
115 BML 0.9528
116 L89 0.9528
117 CIG 0.9528
118 TMZ 0.9527
119 4HS 0.9523
120 6SP 0.9522
121 40O 0.9519
122 1DH 0.9518
123 285 0.9518
124 APY 0.9514
125 ICC 0.9510
126 HTS 0.9510
127 76X 0.9510
128 OXM 0.9508
129 H3M 0.9501
130 DXX 0.9500
131 TMT 0.9498
132 4CH 0.9497
133 2CH 0.9492
134 4H2 0.9485
135 HEW 0.9485
136 4JN 0.9483
137 HGQ 0.9481
138 GOL 0.9479
139 1MR 0.9470
140 BVG 0.9464
141 BVC 0.9460
142 2AF 0.9457
143 6X8 0.9455
144 M3T 0.9439
145 B3R 0.9435
146 SER 0.9434
147 PYJ 0.9433
148 HHQ 0.9432
149 3PY 0.9425
150 OXE 0.9420
151 PYR 0.9419
152 IOL 0.9419
153 9CL 0.9415
154 J1Z 0.9413
155 CYS 0.9412
156 3OH 0.9403
157 DSN 0.9402
158 VAL 0.9396
159 DMG 0.9395
160 OXD 0.9394
161 2EZ 0.9386
162 3MC 0.9384
163 KG7 0.9384
164 URF 0.9381
165 278 0.9381
166 IDH 0.9370
167 HVQ 0.9352
168 YAN 0.9349
169 MLA 0.9345
170 RP7 0.9342
171 LAC 0.9332
172 MLI 0.9331
173 B24 0.9330
174 RSF 0.9330
175 DAL 0.9327
176 GVH 0.9326
177 BZF 0.9324
178 MCT 0.9321
179 HGY 0.9315
180 WBU 0.9313
181 BZI 0.9309
182 2OP 0.9309
183 MLM 0.9308
184 TDR 0.9304
185 IND 0.9299
186 4HO 0.9297
187 1MC 0.9292
188 3FA 0.9291
189 C5J 0.9290
190 FFP 0.9288
191 4JP 0.9286
192 PYD 0.9286
193 ICP 0.9286
194 MAK 0.9284
195 1PT 0.9284
196 0R1 0.9282
197 PYG 0.9276
198 A1U 0.9272
199 MBD 0.9269
200 DEN 0.9269
201 1AC 0.9269
202 PYM 0.9268
203 1DU 0.9267
204 MPI 0.9266
205 FPY 0.9263
206 JZ3 0.9262
207 0CT 0.9261
208 GMN 0.9258
209 275 0.9258
210 LZ1 0.9258
211 TM4 0.9257
212 FLM 0.9256
213 KIV 0.9254
214 MWM 0.9244
215 2C9 0.9239
216 2AC 0.9238
217 ALA 0.9236
218 6MH 0.9231
219 4ZE 0.9225
220 NK 0.9225
221 BR9 0.9225
222 BUO 0.9218
223 3CE 0.9218
224 2MY 0.9215
225 4CL 0.9215
226 27Y 0.9215
227 MZG 0.9213
228 R8A 0.9210
229 XYD 0.9209
230 XBZ 0.9205
231 XYP 0.9203
232 FOA 0.9199
233 DUB 0.9194
234 5UC 0.9189
235 DCY 0.9186
236 4JJ 0.9185
237 2MP 0.9180
238 34A 0.9180
239 YHO 0.9178
240 IDM 0.9174
241 JZ2 0.9174
242 TH0 0.9174
243 OXQ 0.9173
244 PYC 0.9171
245 2RA 0.9170
246 SMB 0.9169
247 TM7 0.9169
248 03W 0.9166
249 4DX 0.9166
250 0R0 0.9163
251 HT4 0.9162
252 4JO 0.9162
253 ABA 0.9160
254 MWJ 0.9160
255 HUI 0.9158
256 NEQ 0.9156
257 PRI 0.9156
258 2CM 0.9155
259 5MH 0.9155
260 5Y9 0.9153
261 WDL 0.9147
262 OHG 0.9145
263 MMU 0.9143
264 AX2 0.9139
265 NIS 0.9137
266 1XX 0.9137
267 6UA 0.9136
268 5JC 0.9135
269 P2D 0.9130
270 JBN 0.9128
271 PRO 0.9128
272 3MH 0.9127
273 LXC 0.9126
274 43M 0.9124
275 2YU 0.9124
276 NAK 0.9122
277 5AC 0.9121
278 A3B 0.9120
279 DBB 0.9120
280 3AY 0.9120
281 BAL 0.9120
282 BEZ 0.9111
283 THR 0.9109
284 5AN 0.9100
285 TZC 0.9099
286 MEU 0.9097
287 NCM 0.9096
288 NCA 0.9095
289 BEN 0.9094
290 5ZE 0.9090
291 JZ1 0.9085
292 HY3 0.9085
293 IUR 0.9080
294 XYS 0.9080
295 QOS 0.9079
296 286 0.9079
297 2ZX 0.9077
298 MLT 0.9073
299 GAG 0.9072
300 GBD 0.9071
301 13X 0.9071
302 GOA 0.9067
303 AHR 0.9064
304 NIO 0.9062
305 HBA 0.9057
306 6PC 0.9051
307 0TR 0.9050
308 SMV 0.9050
309 YCP 0.9048
310 BAM 0.9043
311 JAB 0.9043
312 94N 0.9043
313 PZA 0.9041
314 2PC 0.9040
315 Y8I 0.9039
316 39J 0.9034
317 GLV 0.9030
318 ALO 0.9029
319 23W 0.9025
320 AKR 0.9023
321 C2A 0.9023
322 265 0.9023
323 TLD 0.9021
324 BP9 0.9021
325 NBZ 0.9019
326 9X7 0.9017
327 LDU 0.9012
328 IT2 0.9010
329 192 0.9010
330 JZ9 0.9010
331 VGL 0.9009
332 2HA 0.9006
333 ERH 0.9004
334 BUA 0.9004
335 FAH 0.9000
336 TP5 0.8992
337 RIB 0.8985
338 TFB 0.8981
339 R2B 0.8978
340 RIP 0.8978
341 PZO 0.8974
342 M58 0.8972
343 BR8 0.8970
344 HAE 0.8970
345 JIF 0.8963
346 7CZ 0.8961
347 GXV 0.8959
348 3GR 0.8951
349 C2N 0.8949
350 ALQ 0.8949
351 273 0.8949
352 SS2 0.8948
353 2DR 0.8948
354 LER 0.8948
355 IMD 0.8947
356 NIE 0.8945
357 SAR 0.8942
358 HUH 0.8940
359 1AB 0.8938
360 UNU 0.8937
361 PHB 0.8937
362 NHY 0.8935
363 TRI 0.8934
364 GLY 0.8933
365 C21 0.8933
366 BAE 0.8932
367 NTN 0.8929
368 4VP 0.8929
369 4JL 0.8926
370 R1X 0.8924
371 ADE 0.8921
372 QSC 0.8919
373 F50 0.8916
374 IMR 0.8911
375 EDG 0.8909
376 0MK 0.8909
377 6MP 0.8908
378 AGU 0.8906
379 HVB 0.8905
380 47J 0.8905
381 HPA 0.8904
382 C2B 0.8903
383 9DA 0.8903
384 PPI 0.8902
385 PM6 0.8898
386 HBS 0.8898
387 NMU 0.8888
388 MGX 0.8888
389 FUC 0.8887
390 JZ5 0.8886
391 23A 0.8885
392 AKB 0.8883
393 64K 0.8883
394 7HP 0.8881
395 60P 0.8880
396 FBA 0.8880
397 T2C 0.8877
398 H8N 0.8876
399 9TY 0.8876
400 ES4 0.8875
401 BP1 0.8874
402 TCZ 0.8867
403 2A1 0.8865
404 HSE 0.8862
405 F3V 0.8860
406 9HX 0.8859
407 AC0 0.8859
408 CHT 0.8858
409 DAB 0.8858
410 PBC 0.8857
411 AAE 0.8853
412 ARB 0.8850
413 4XR 0.8850
414 ASP 0.8847
415 ARA 0.8846
416 DFB 0.8840
417 10L 0.8840
418 7MH 0.8839
419 DPR 0.8835
420 FUL 0.8832
421 PAE 0.8830
422 CP 0.8829
423 7WA 0.8825
424 MAE 0.8825
425 61G 0.8824
426 4JM 0.8824
427 FLA 0.8823
428 270 0.8820
429 TF4 0.8820
430 R3W 0.8820
431 IFM 0.8820
432 M2H 0.8817
433 HSM 0.8815
434 AOA 0.8812
435 YTB 0.8810
436 MZW 0.8808
437 MRY 0.8806
438 SS1 0.8806
439 BTE 0.8799
440 AZF 0.8798
441 O7U 0.8797
442 DFU 0.8795
443 BU4 0.8795
444 RUU 0.8794
445 PCA 0.8793
446 2HE 0.8790
447 51F 0.8787
448 F81 0.8781
449 P92 0.8780
450 KYD 0.8777
451 OAA 0.8773
452 HCS 0.8773
453 T6C 0.8768
454 IQ0 0.8762
455 BMD 0.8761
456 FW5 0.8760
457 6HQ 0.8760
458 2MI 0.8759
459 OXZ 0.8759
460 1WD 0.8758
461 3XX 0.8757
462 3Z7 0.8753
463 PEA 0.8753
464 LMR 0.8749
465 JBE 0.8745
466 FAN 0.8745
467 ETF 0.8745
468 SAL 0.8744
469 RSO 0.8737
470 CRN 0.8737
471 IP0 0.8736
472 TAY 0.8732
473 14J 0.8730
474 BNS 0.8727
475 F05 0.8724
476 PBE 0.8722
477 HLT 0.8721
478 NMJ 0.8721
479 BUQ 0.8718
480 AX7 0.8717
481 9YL 0.8716
482 PPF 0.8708
483 3U4 0.8706
484 BZX 0.8705
485 H76 0.8704
486 ABE 0.8703
487 TSZ 0.8702
488 ITN 0.8698
489 ATO 0.8698
490 6AI 0.8695
491 DTL 0.8695
492 PRS 0.8694
493 DTU 0.8693
494 FUF 0.8691
495 FYU 0.8690
496 HLR 0.8690
497 69O 0.8689
498 9EW 0.8687
499 3HR 0.8686
500 VNJ 0.8683
501 CEE 0.8682
502 4SV 0.8681
503 ZZT 0.8677
504 271 0.8674
505 BE2 0.8674
506 QUZ 0.8673
507 AGK 0.8670
508 CIZ 0.8670
509 SVN 0.8668
510 PXO 0.8666
511 TBP 0.8663
512 ALF 0.8660
513 8NY 0.8660
514 SSN 0.8659
515 H4N 0.8657
516 24B 0.8657
517 ES6 0.8652
518 PEL 0.8649
519 3SK 0.8646
520 ITU 0.8643
521 0RW 0.8642
522 5H1 0.8641
523 3HL 0.8638
524 PAV 0.8634
525 NPY 0.8633
526 ES9 0.8631
527 FK1 0.8630
528 FUB 0.8629
529 KOJ 0.8625
530 HMH 0.8622
531 1DQ 0.8622
532 S76 0.8621
533 HV2 0.8620
534 260 0.8619
535 HY1 0.8618
536 HYP 0.8615
537 5MI 0.8614
538 BXA 0.8611
539 GIF 0.8610
540 11S 0.8610
541 5MB 0.8608
542 1DW 0.8608
543 2K4 0.8604
544 SIN 0.8600
545 BRP 0.8598
546 Z6J 0.8590
547 150 0.8584
548 F60 0.8581
549 14O 0.8581
550 CSS 0.8574
551 JZ7 0.8572
552 4ZC 0.8571
553 JKE 0.8570
554 45C 0.8570
555 MTG 0.8569
556 ZZ3 0.8559
557 ABV 0.8554
558 FCN 0.8552
559 261 0.8544
560 MRZ 0.8540
561 35C 0.8539
562 HX3 0.8528
563 7WV 0.8528
564 FCA 0.8520
565 2CQ 0.8520
566 SGL 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4CC6; Ligand: L5Y; 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: 4cc6.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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