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Receptor
PDB id Resolution Class Description Source Keywords
5FQK 1.77 Å EC: 3.5.2.6 W229D AND F290W MUTANT OF THE LAST COMMON ANCESTOR OF GRAM-N BACTERIA (GNCA4) BETA-LACTAMASE CLASS A BOUND TO 5(6)- N ITROBENZOTRIAZOLE (TS-ANALOG) SYNTHETIC CONSTRUCT HYDROLASE PRECAMBRIAN RESURRECTED BETA-LACTAMASE GNCA4
Ref.: DE NOVO ACTIVE SITES FOR RESURRECTED PRECAMBRIAN EN NAT COMMUN V. 8 16113 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6NT A:301;
Valid;
none;
Kd = 15.8 uM
164.122 C6 H4 N4 O2 c1cc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FQK 1.77 Å EC: 3.5.2.6 W229D AND F290W MUTANT OF THE LAST COMMON ANCESTOR OF GRAM-N BACTERIA (GNCA4) BETA-LACTAMASE CLASS A BOUND TO 5(6)- N ITROBENZOTRIAZOLE (TS-ANALOG) SYNTHETIC CONSTRUCT HYDROLASE PRECAMBRIAN RESURRECTED BETA-LACTAMASE GNCA4
Ref.: DE NOVO ACTIVE SITES FOR RESURRECTED PRECAMBRIAN EN NAT COMMUN V. 8 16113 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
2 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
2 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
4 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
5 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
6 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
7 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
8 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
9 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
10 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
11 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
12 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
13 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
14 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
15 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
16 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
17 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
18 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
19 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
20 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
21 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
22 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
23 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
24 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
25 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
26 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
27 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
28 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
29 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
30 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
31 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
32 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
33 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
34 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
35 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
36 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
37 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
38 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
39 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
40 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
41 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
42 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6NT; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6NT 1 1
2 3NY 0.5 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FQK; Ligand: 6NT; Similar sites found with APoc: 384
This union binding pocket(no: 1) in the query (biounit: 5fqk.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2D6M LBT None
2 1HBK COA None
3 1MID LAP None
4 2FR6 URI None
5 1MQ0 BRD None
6 2GBB CIT None
7 2FR6 CTN None
8 4JH6 FCN None
9 5Y02 MXN None
10 1H9G COA MYR 0.823045
11 4IAW LIZ 1.06383
12 1M3U KPL 1.13636
13 1W8S FBP 1.14068
14 4OCV ANP 1.48699
15 3HAV ATP 1.48699
16 3G5D 1N1 1.48699
17 2YOO K2B 1.48699
18 4P7X YCP 1.48699
19 4P7X AKG 1.48699
20 4Z28 BTN 1.49254
21 3H7J PPY 1.64609
22 3WR7 COA 1.76471
23 4OCT AKG 1.8018
24 5YU3 NAD 1.85874
25 5YU3 PRO 1.85874
26 1VPV PLM 1.85874
27 1MGP PLM 1.85874
28 3V4S ATP 1.85874
29 5H2D ERG 1.85874
30 2IVN ANP 1.85874
31 3FYS PLM 1.85874
32 5IGI GMP 1.85874
33 5IGI ZIT 1.85874
34 4DHY S41 1.85874
35 5J75 6GQ 1.89394
36 5JSP DQY 1.99005
37 5URY PAM 2.05479
38 3SFI 3SF 2.11864
39 4QA8 PJZ 2.18341
40 5KBE IPH 2.18341
41 6EOZ AKG 2.23048
42 6EOZ 58K 2.23048
43 4WO4 JLS 2.23048
44 2XFH CL6 2.23048
45 4N14 WR7 2.23048
46 4NZN 2OU 2.23048
47 4NZN ANP 2.23048
48 5HGR 45D 2.23048
49 6B2M COA 2.23048
50 2HFN FMN 2.23048
51 2X5W K2B 2.23048
52 1OS7 TAU 2.23048
53 1OS7 AKG 2.23048
54 1WUB OTP 2.24719
55 6BA2 7KM 2.37288
56 4COQ SAN 2.42915
57 3I8T LBT 2.43902
58 4TWL ASC 2.43902
59 3SAO DBH 2.5
60 3SAO NKN 2.5
61 2OBD PCW 2.60223
62 3QCP FAD 2.60223
63 3W0O ADP 2.60223
64 3W0O HY0 2.60223
65 2XK9 XK9 2.60223
66 1KJ8 ATP 2.60223
67 1KJ8 GAR 2.60223
68 1PS9 FAD 2.60223
69 1ODM ASV 2.60223
70 3OV6 MK0 2.60223
71 3ICS COA 2.60223
72 3OZV ECN 2.60223
73 5MBC FMN 2.60223
74 2OBD 2OB 2.60223
75 4E1O PLP PVH 2.60223
76 2Z9I GLY ALA THR VAL 2.60223
77 2OO8 RAJ 2.60223
78 1XIM XYL 2.60223
79 4XB4 45D 2.63158
80 3KP6 SAL 2.64901
81 5HCV 60R 2.72374
82 5NI5 8YB 2.77778
83 1W3R PYR 2.77778
84 4N7C AEF 2.84091
85 3WUC GLC GAL 2.91971
86 6BYM HC3 2.95567
87 1ZHX HC3 2.97398
88 2HHJ 3PG 2.97398
89 2HHJ DG2 2.97398
90 5W4W 9WG 2.97398
91 3A7R LAQ 2.97398
92 4C0C WVH 2.97398
93 5FBN 5WF 2.97398
94 4YZC STU 2.97398
95 4IA6 EIC 2.97398
96 1T27 PCW 2.97398
97 1GQG DCD 2.97398
98 1M13 HYF 2.97398
99 4E5N NAD 2.97398
100 4L9Z COA 2.97398
101 5FOI MY8 2.97398
102 3FW3 ETS 3.00752
103 6AYI C3G 3.01508
104 5APK 76E 3.01887
105 4WPF 3SN 3.0303
106 3PFG SAM 3.04183
107 3PFG TLO 3.04183
108 6D61 4AA 3.07692
109 2JIG PD2 3.125
110 2PVN P63 3.125
111 3T50 FMN 3.125
112 2GC0 PAN 3.19149
113 4G8R 96P 3.19149
114 1EYE PMM 3.21429
115 3MTX PGT 3.31126
116 5KJZ PCG 3.33333
117 4TWP AXI 3.34572
118 5Y79 3PG 3.34572
119 1E8G FCR 3.34572
120 1NHZ 486 3.34572
121 3ETH ATP 3.34572
122 1XLI GLT 3.34572
123 6AYH C3G 3.34572
124 1RQJ RIS 3.34572
125 5C1M 4VO 3.34572
126 5NTP 98E 3.36134
127 5UWA 8ND 3.44828
128 1QY1 PRZ 3.44828
129 5IXK 6EW 3.50877
130 3PG7 PTY 3.51562
131 3KXC PLM 3.60825
132 4H69 10Y 3.60825
133 1A8R GTP 3.61991
134 5KAU RHQ 3.63636
135 5N18 8HZ 3.66972
136 4D7M TDC 3.68664
137 2BL9 CP6 3.71747
138 2BL9 NDP 3.71747
139 3WVS RRM 3.71747
140 1N1G BCP 3.71747
141 4J36 1HR 3.71747
142 3HX3 RET 3.71747
143 3PFD FDA 3.71747
144 6FXR AKG 3.71747
145 2ACV UDP 3.71747
146 3AKK ADP 3.71747
147 1KQR MNA 3.71747
148 1EGD FAD 3.71747
149 2PUL ACP 3.71747
150 5W99 A1V 3.71747
151 3VPB ADP 3.71747
152 3BEO UDP 3.71747
153 2HFP NSI 3.71747
154 2YPO PHE 3.71747
155 3VPC ADP 3.71747
156 3CLH NAD 3.71747
157 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 3.7234
158 2P3I MNA 3.72671
159 3E2M E2M 3.78378
160 4WX0 HXD 3.80228
161 1QIN GIP 3.82514
162 4WW7 AMP 3.83142
163 2Q1H AS4 4
164 5B4B LP5 4.03226
165 5UC1 486 4.05405
166 6FOF LAT 4.08163
167 5Y9D FAD 4.08922
168 5NJI 8Z2 4.08922
169 2R5V HHH 4.08922
170 3DAG FEG 4.08922
171 1B4U DHB 4.08922
172 1ZB6 GST 4.08922
173 5Z21 NAI 4.08922
174 5X7Q GLC GLC GLC GLC GLC 4.08922
175 4K90 MLA 4.08922
176 1D1G NDP 4.16667
177 4YGF AZM 4.2735
178 6FE1 V14 4.28016
179 4X5S AZM 4.31034
180 3JRS A8S 4.32692
181 3FS1 MYR 4.34783
182 1UVC STE 4.3956
183 4MNS 2AX 4.40252
184 3EW2 BTN 4.44444
185 3KDJ A8S 4.45545
186 2V58 LZJ 4.46097
187 3NTD COA 4.46097
188 2Y3S TIR 4.46097
189 3RY9 1CA 4.46097
190 3NT6 COA 4.46097
191 3K5I ADP 4.46097
192 4H6Q TFB 4.46097
193 4BVA T3 4.47761
194 3HB5 E2B 4.58716
195 3HB5 NAP 4.58716
196 5LJ0 6XX 4.61538
197 6FS0 E4W 4.65116
198 5VM0 9EG 4.6875
199 1Y0G 8PP 4.71204
200 3CF6 SP1 4.79042
201 5UI2 EQ3 4.83271
202 3NRR D16 4.83271
203 2P1C GG3 4.83271
204 5IKH 6BW 4.83271
205 5EY0 GTP 4.83271
206 6C1R EFD 4.83271
207 1HG4 LPP 4.83271
208 6CS8 F9Y 4.83271
209 4K55 H6P 4.83871
210 5KEW 6SB 4.86111
211 2OKL BB2 4.86486
212 5IDB BMA 4.92958
213 5ECP ATP 4.93274
214 5UR6 8KM 4.97238
215 3WV6 GAL BGC 5.20446
216 3GL0 HXX 5.20446
217 5DXT 5H5 5.20446
218 6GN6 MAL 5.20446
219 1SO0 GAL 5.20446
220 5XQW 8EU 5.20446
221 5NW7 9C2 5.20446
222 5AE9 OKO 5.20446
223 3ZJ0 ACO 5.33981
224 2HKA C3S 5.38462
225 5NBW 8SK 5.40541
226 5N5U 7N8 5.41401
227 5N5U AMP 5.41401
228 2VBQ BSJ 5.45455
229 6CC0 EWM 5.48523
230 5I0U DCY 5.5
231 5HV0 AKG 5.52995
232 2AGC DAO 5.55556
233 4AZW ATP 5.57621
234 1EWF PC1 5.57621
235 1OAA OAA 5.57621
236 2XN5 FUN 5.57621
237 2XN3 ID8 5.57621
238 5CJH 522 5.57621
239 3EKK GS2 5.57621
240 4JWH SAH 5.57621
241 4KS7 X4Z 5.57621
242 5A61 3PO 5.57621
243 4IXH IMP 5.57621
244 5C5T AKG 5.57621
245 4C5N ACP 5.7971
246 4C5N PXL 5.7971
247 2E27 AB0 5.88235
248 1XVB BHL 5.88235
249 5JF2 SF7 5.88235
250 4LRJ ANP 5.91716
251 5U9J GER 5.91716
252 5DRB 5FJ 5.94796
253 3LLI FAD 5.94796
254 3T58 FAD 5.94796
255 3E8T UQ8 5.94796
256 4PFC 2QX 5.94796
257 6C7D EOJ 5.94796
258 3G5N PB2 5.94796
259 3ZDS HMQ 5.94796
260 1A27 EST 5.94796
261 1G27 BB1 5.95238
262 1A78 TDG 5.97015
263 5T2Z 017 6.06061
264 1N4H REA 6.17761
265 4REF 3N0 6.25
266 1GNI OLA 6.3197
267 6C0B PAM 6.3197
268 5C4L 4XR 6.3197
269 2OVD DAO 6.3197
270 3U3U EAH 6.3197
271 5FXD H7Y 6.3197
272 4X9X OLA 6.3197
273 4EIL FOL 6.3197
274 4LA7 A1O 6.34441
275 2Y7P SAL 6.42202
276 2YIP YIO 6.52174
277 5A67 3PO 6.60377
278 4K49 HFQ 6.61765
279 3WUD GLC GAL 6.61765
280 5DG2 GAL GLC 6.66667
281 3WVR AMP 6.69145
282 2H7C COA 6.69145
283 1OGX EQU 6.87023
284 4JWF SAH 6.91244
285 3RET PYR 6.93069
286 3RET SAL 6.93069
287 2E56 MYR 6.94444
288 6D6L FY4 7.05882
289 4NFN 2KC 7.0632
290 3B9Z CO2 7.0632
291 4OIC A8S 7.0632
292 2PYW ADP 7.0632
293 5WRE 7TL 7.09677
294 3QP4 HL0 7.14286
295 3OG9 MLT 7.17703
296 6C7R EO4 7.2
297 1TT8 PHB 7.31707
298 4U0W 16G 7.31707
299 1Q1Y BB2 7.32984
300 4ZU4 4TG 7.43243
301 2VQD AP2 7.43494
302 2YKL NLD 7.43494
303 5ZM4 9FU 7.43494
304 1U59 STU 7.43494
305 6F6D AKG 7.43494
306 1AL8 DHP 7.43494
307 2YJD YJD 7.43494
308 5CYV WCA 7.53425
309 5LOF 70R 7.80669
310 5NKB 8ZT 7.80669
311 1ZPD CIT 7.80669
312 1J3R 6PG 7.80669
313 3N0Y APC 7.82123
314 4Y8D 49J 7.85714
315 3OJI PYV 7.93651
316 5NNT DPV 8.10811
317 3QP8 HL0 8.15217
318 5C3R HMU 8.17844
319 5C3R AKG 8.17844
320 2AMT 1AA 8.17844
321 3B99 U51 8.17844
322 2PCU ASP 8.17844
323 4QDC ASD 8.20513
324 2E3N 6CM 8.23529
325 3RMK BML 8.43373
326 1DMY AZM 8.46774
327 1MDC PLM 8.55019
328 5ML3 DL3 8.55019
329 6BXI ANP 8.55019
330 5L9G MO0 8.55019
331 1Y9Q MED 8.85417
332 5ANU 58T 8.86076
333 4DP3 NDP 8.92193
334 4MZU COA 8.92193
335 1XXA ARG 8.97436
336 3ZXE PGZ 9.02256
337 3DFR MTX 9.25926
338 3KDU NKS 9.29368
339 2P54 735 9.29368
340 2AG4 OLA 9.29368
341 2NPA MMB 9.29368
342 1K7L 544 9.29368
343 1CX4 CMP 9.66543
344 6C0T EE4 9.66543
345 3G08 FEE 10.0372
346 4RVU NDP 10.0372
347 5SVV FMN 10.0372
348 1GUX ASP LEU TYR CYS TYR GLU GLN LEU ASN 10.0917
349 3U7S 017 10.101
350 3WG3 A2G GAL NAG FUC 10.1124
351 5ICK FEZ 10.4089
352 5T8U LPA 10.4089
353 3BEJ MUF 10.4089
354 1YRX FMN 10.7438
355 3PP0 03Q 10.7807
356 5E2N V14 11.0266
357 4WHZ 3NL 11.1524
358 3M3E GAL A2G NPO 11.1524
359 3FW4 CAQ 11.236
360 4WN5 MVC 11.3043
361 1FM9 9CR 11.3445
362 4POJ 2VP 11.6883
363 6GG9 FMN 11.7284
364 3VV1 GAL FUC 11.875
365 2NPX FAD 11.8959
366 4PFO ADP 11.8959
367 1LQY BB2 12.5
368 2XXP DSL 13.0112
369 1WPY BTN 14.4681
370 5K2M ADP 15.0943
371 4RJD TFP 15.1515
372 5YS9 FAD 15.6134
373 4EOX 0S5 15.9851
374 4RLT FSE 17.6871
375 2QZT PLM 18.018
376 1DZK PRZ 19.1083
377 1PVN MZP 22.6766
378 5X8Q 82R 22.7273
379 1NU4 MLA 23.7113
380 2DYS TGL 28.2609
381 5Z84 TGL 28.2609
382 2DYR TGL 28.2609
383 5Z84 CHD 28.2609
384 5ZCO TGL 28.2609
385 5G5W R8C 50
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