-->
Receptor
PDB id Resolution Class Description Source Keywords
5CFT 1.5 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ANT(2")-IA IN COMPLEX WITH AMPCPP AND G C1 PSEUDOMONAS AERUGINOSA ANTIBIOTIC RESISTANCE NUCLEOTIDYLTRANSFERASE AMPCPP GENTAROSSMANN FOLD TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: STRUCTURAL ANALYSIS OF THE TOBRAMYCIN AND GENTAMICI CLINICAL RESISTOME REVEALS LIMITATIONS FOR NEXT-GEN AMINOGLYCOSIDE DESIGN. ACS CHEM.BIOL. V. 11 1339 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
APC A:203;
Valid;
none;
submit data
505.208 C11 H18 N5 O12 P3 c1nc(...
MN A:201;
A:202;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
51G A:204;
Valid;
none;
submit data
477.595 C21 H43 N5 O7 C[C@H...
P6G A:205;
Invalid;
none;
submit data
282.331 C12 H26 O7 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CFT 1.5 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ANT(2")-IA IN COMPLEX WITH AMPCPP AND G C1 PSEUDOMONAS AERUGINOSA ANTIBIOTIC RESISTANCE NUCLEOTIDYLTRANSFERASE AMPCPP GENTAROSSMANN FOLD TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: STRUCTURAL ANALYSIS OF THE TOBRAMYCIN AND GENTAMICI CLINICAL RESISTOME REVEALS LIMITATIONS FOR NEXT-GEN AMINOGLYCOSIDE DESIGN. ACS CHEM.BIOL. V. 11 1339 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 5CFT - 51G C21 H43 N5 O7 C[C@H]([C@....
2 5CFS - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 5CFT - 51G C21 H43 N5 O7 C[C@H]([C@....
2 5CFS - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 5CFT - 51G C21 H43 N5 O7 C[C@H]([C@....
2 5CFS - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: APC; Similar ligands found: 345
No: Ligand ECFP6 Tc MDL keys Tc
1 APC 1 1
2 ACQ 0.831169 0.986301
3 AP2 0.821918 1
4 A12 0.821918 1
5 ADV 0.805195 0.972973
6 RBY 0.805195 0.972973
7 AMP 0.777778 0.931507
8 A 0.777778 0.931507
9 ADP 0.763158 0.958904
10 ACP 0.75641 0.986301
11 6YZ 0.756098 0.986301
12 A2D 0.746667 0.932432
13 AP5 0.74026 0.932432
14 B4P 0.74026 0.932432
15 HEJ 0.734177 0.958904
16 ATP 0.734177 0.958904
17 BA3 0.727273 0.932432
18 5FA 0.725 0.958904
19 AQP 0.725 0.958904
20 ABM 0.723684 0.881579
21 AT4 0.708861 0.921053
22 AN2 0.708861 0.945946
23 M33 0.7 0.92
24 T99 0.698795 0.921053
25 TAT 0.698795 0.921053
26 SRA 0.697368 0.883117
27 AR6 0.682927 0.932432
28 APR 0.682927 0.932432
29 ADX 0.679012 0.841463
30 CA0 0.679012 0.907895
31 AU1 0.679012 0.933333
32 ANP 0.678571 0.933333
33 AD9 0.674699 0.933333
34 SAP 0.674699 0.909091
35 AGS 0.674699 0.909091
36 ADP PO3 0.674699 0.905405
37 50T 0.670732 0.92
38 PRX 0.662651 0.858974
39 ATF 0.643678 0.921053
40 MAP 0.640449 0.909091
41 A22 0.640449 0.945946
42 GAP 0.639535 0.858974
43 TAD 0.632653 0.923077
44 5AL 0.632184 0.894737
45 SON 0.626506 0.946667
46 ADQ 0.626374 0.907895
47 ALF ADP 0.625 0.8375
48 ADP ALF 0.625 0.8375
49 LMS 0.620253 0.797619
50 VO4 ADP 0.617977 0.894737
51 SRP 0.617977 0.896104
52 ADP VO4 0.617977 0.894737
53 9ZA 0.615385 0.873418
54 25A 0.615385 0.932432
55 9ZD 0.615385 0.873418
56 XYA 0.611111 0.810811
57 RAB 0.611111 0.810811
58 ADN 0.611111 0.810811
59 25L 0.610526 0.945946
60 4AD 0.608696 0.909091
61 A3R 0.608696 0.922078
62 A1R 0.608696 0.922078
63 DAL AMP 0.604396 0.87013
64 OOB 0.597826 0.894737
65 8QN 0.597826 0.894737
66 5SV 0.597826 0.839506
67 9X8 0.595745 0.884615
68 OAD 0.595745 0.907895
69 ADP BMA 0.595745 0.883117
70 AMO 0.591398 0.921053
71 PAJ 0.591398 0.851852
72 AOC 0.585366 0.789474
73 00A 0.585106 0.85
74 AHX 0.585106 0.886076
75 DLL 0.585106 0.894737
76 PTJ 0.583333 0.8625
77 3OD 0.583333 0.907895
78 BIS 0.583333 0.897436
79 3UK 0.578947 0.883117
80 DZD 0.577982 0.923077
81 5AS 0.576471 0.752809
82 5N5 0.573333 0.786667
83 PR8 0.572917 0.864198
84 WAQ 0.572917 0.897436
85 LAD 0.572917 0.875
86 B5V 0.572917 0.871795
87 4TC 0.571429 0.910256
88 TXA 0.56701 0.896104
89 NB8 0.56701 0.886076
90 1ZZ 0.56701 0.831325
91 FYA 0.56701 0.894737
92 ME8 0.56701 0.831325
93 A4D 0.565789 0.786667
94 5CD 0.565789 0.773333
95 ATP A A A 0.565657 0.893333
96 A3P 0.564706 0.931507
97 7D5 0.5625 0.868421
98 PAP 0.561798 0.945205
99 MYR AMP 0.561224 0.809524
100 G5P 0.558824 0.886076
101 M2T 0.556962 0.707317
102 A A 0.556701 0.906667
103 9SN 0.555556 0.839506
104 G2P 0.553191 0.923077
105 7D3 0.552941 0.894737
106 UP5 0.552381 0.884615
107 TXD 0.552381 0.873418
108 JB6 0.55102 0.873418
109 2A5 0.550562 0.907895
110 FA5 0.55 0.896104
111 YAP 0.55 0.884615
112 B5Y 0.55 0.860759
113 B5M 0.55 0.860759
114 G3A 0.54902 0.886076
115 3AM 0.548781 0.891892
116 A2P 0.546512 0.917808
117 7D4 0.545455 0.894737
118 XAH 0.544554 0.853659
119 ATR 0.544444 0.931507
120 EP4 0.544304 0.725
121 AFH 0.543689 0.875
122 GA7 0.543689 0.896104
123 4UV 0.539216 0.860759
124 TYR AMP 0.539216 0.860759
125 GTA 0.538462 0.853659
126 DQV 0.538462 0.92
127 G5A 0.538462 0.772727
128 NAI 0.537736 0.873418
129 DTA 0.5375 0.779221
130 3DH 0.536585 0.74359
131 LAQ 0.533333 0.831325
132 AHZ 0.533333 0.788235
133 MTA 0.530864 0.74359
134 ARG AMP 0.528846 0.821429
135 4UU 0.528846 0.860759
136 7MD 0.528846 0.853659
137 AR6 AR6 0.528846 0.881579
138 48N 0.528302 0.886076
139 LPA AMP 0.528302 0.809524
140 ITT 0.52809 0.905405
141 AMP DBH 0.524272 0.858974
142 NAX 0.523364 0.864198
143 4UW 0.523364 0.829268
144 DND 0.523364 0.896104
145 NXX 0.523364 0.896104
146 6V0 0.523364 0.8625
147 IMO 0.523256 0.891892
148 A4P 0.522936 0.813953
149 HFD 0.521739 0.909091
150 A5A 0.521277 0.77907
151 TSB 0.520833 0.790698
152 TXE 0.518519 0.873418
153 OMR 0.518519 0.843373
154 2AM 0.518072 0.905405
155 6RE 0.517647 0.753086
156 S4M 0.517241 0.681818
157 V3L 0.516129 0.932432
158 SSA 0.515789 0.793103
159 YLP 0.514019 0.833333
160 AP0 0.513761 0.8625
161 UPA 0.513761 0.873418
162 139 0.513514 0.864198
163 T5A 0.513514 0.855422
164 PPS 0.510638 0.841463
165 VMS 0.510417 0.761364
166 A2R 0.510417 0.945946
167 54H 0.510417 0.761364
168 52H 0.510417 0.752809
169 CNA 0.508929 0.896104
170 ZAS 0.505882 0.7375
171 J7C 0.505747 0.7625
172 A3N 0.505747 0.75641
173 5X8 0.505495 0.75641
174 8X1 0.505155 0.747253
175 53H 0.505155 0.752809
176 5CA 0.505155 0.793103
177 TYM 0.504587 0.896104
178 AF3 ADP 3PG 0.504587 0.829268
179 IOT 0.504505 0.845238
180 80F 0.504348 0.833333
181 ADJ 0.5 0.843373
182 7MC 0.5 0.833333
183 AMP NAD 0.5 0.87013
184 OVE 0.5 0.87013
185 YLC 0.5 0.853659
186 YLB 0.5 0.833333
187 P5A 0.49505 0.758242
188 NSS 0.494949 0.793103
189 DSZ 0.494949 0.793103
190 LSS 0.494949 0.755556
191 6AD 0.494737 0.875
192 MAO 0.494382 0.77381
193 DSH 0.494253 0.740741
194 A3D 0.491379 0.883117
195 F2R 0.491228 0.855422
196 9K8 0.490196 0.691489
197 NVA LMS 0.49 0.747253
198 AV2 0.489583 0.881579
199 COD 0.486957 0.825581
200 4TA 0.486957 0.821429
201 NAD 0.486957 0.894737
202 YLA 0.486726 0.833333
203 LEU LMS 0.485149 0.747253
204 NA7 0.485149 0.972973
205 3AT 0.484211 0.958904
206 GJV 0.483146 0.743902
207 AYB 0.482456 0.823529
208 5AD 0.480519 0.716216
209 KAA 0.480392 0.766667
210 GSU 0.480392 0.772727
211 71V 0.477778 0.873418
212 A3G 0.477273 0.792208
213 7D7 0.474359 0.736842
214 G A A A 0.474138 0.839506
215 BTX 0.474138 0.855422
216 6C6 0.473684 0.896104
217 SFG 0.473118 0.766234
218 DAT 0.473118 0.92
219 YSA 0.471698 0.772727
220 PO4 PO4 A A A A PO4 0.470588 0.866667
221 BT5 0.470085 0.845238
222 AVV 0.47 0.910256
223 SMM 0.469388 0.701149
224 SAM 0.46875 0.705882
225 6IA 0.46875 0.829268
226 DTP 0.46875 0.92
227 A7D 0.467391 0.792208
228 M24 0.466667 0.819277
229 SA8 0.463158 0.722892
230 A5D 0.463158 0.779221
231 NAE 0.46281 0.860759
232 MHZ 0.462366 0.712644
233 PGS 0.462366 0.85
234 8PZ 0.462264 0.793103
235 NAJ PZO 0.462185 0.817073
236 DA 0.460674 0.893333
237 D5M 0.460674 0.893333
238 NEC 0.460674 0.717949
239 EAD 0.459677 0.841463
240 2SA 0.459184 0.921053
241 NAQ 0.459016 0.839506
242 SAH 0.458333 0.759494
243 SAI 0.458333 0.75
244 Y3J 0.45679 0.697368
245 A A A 0.456311 0.92
246 AAM 0.455556 0.931507
247 6K6 0.455446 0.893333
248 ZID 0.455285 0.883117
249 S7M 0.454545 0.705882
250 YLY 0.454545 0.823529
251 4YB 0.454545 0.755556
252 AMZ 0.453488 0.88
253 C2R 0.453488 0.868421
254 A3S 0.451613 0.802632
255 Z5A 0.451613 0.772727
256 7DD 0.451613 0.945205
257 U A 0.45 0.873418
258 7C5 0.449541 0.7875
259 101 0.449438 0.868421
260 A G 0.449153 0.85
261 EEM 0.44898 0.705882
262 NAJ PYZ 0.447154 0.77907
263 N6P 0.446602 0.878378
264 ARU 0.446602 0.829268
265 AIR 0.445783 0.864865
266 U A G G 0.445378 0.85
267 P1H 0.445312 0.821429
268 NDE 0.445312 0.896104
269 N0B 0.443548 0.833333
270 A U 0.443478 0.8375
271 NIA 0.443182 0.792683
272 A3T 0.442105 0.789474
273 GEK 0.441176 0.753086
274 GP2 0.438776 0.923077
275 DDS 0.438776 0.868421
276 WSA 0.438596 0.781609
277 7DT 0.4375 0.945205
278 0WD 0.436975 0.886076
279 8BR 0.434783 0.871795
280 AAT 0.434343 0.722892
281 TXP 0.432203 0.886076
282 GGZ 0.431373 0.795181
283 NJP 0.428571 0.909091
284 A6D 0.428571 0.717647
285 FB0 0.427481 0.83908
286 NDC 0.427481 0.8625
287 649 0.426087 0.758242
288 7RA 0.423913 0.918919
289 NDP 0.423729 0.886076
290 0UM 0.423077 0.714286
291 8Q2 0.422414 0.766667
292 QQY 0.422222 0.78481
293 ACK 0.422222 0.826667
294 RGT 0.422018 0.921053
295 FDA 0.421053 0.825581
296 CC5 0.419753 0.808219
297 ANZ 0.419643 0.771084
298 62X 0.419048 0.681818
299 APU 0.418803 0.860759
300 6FA 0.41791 0.833333
301 128 0.417391 0.75
302 ODP 0.416667 0.875
303 3AD 0.416667 0.797297
304 TM1 0.416667 0.747126
305 K15 0.415094 0.697674
306 2BA 0.414894 0.878378
307 CMP 0.414894 0.864865
308 V1N 0.414414 0.881579
309 S8M 0.413462 0.775
310 7RP 0.413043 0.890411
311 2VA 0.412371 0.769231
312 12D 0.412281 0.758621
313 NPW 0.411765 0.876543
314 SFD 0.411765 0.729167
315 FAS 0.411765 0.843373
316 FAD 0.411765 0.843373
317 2FA 0.411765 0.782051
318 QQX 0.411111 0.775
319 62F 0.410072 0.853659
320 AS 0.408602 0.848101
321 FAI 0.408602 0.88
322 RMB 0.408602 0.837838
323 NZQ 0.408333 0.898734
324 GCP 0.407767 0.910256
325 SXZ 0.407407 0.72619
326 RP1 0.406593 0.810127
327 SP1 0.406593 0.810127
328 EO7 0.404255 0.761364
329 NVA 2AD 0.40404 0.753086
330 D3Y 0.403846 0.782051
331 KB1 0.40367 0.714286
332 A C A C 0.403226 0.817073
333 SLU 0.403226 0.744444
334 N01 0.403226 0.87013
335 G 0.402062 0.871795
336 5GP 0.402062 0.871795
337 XNP 0.401639 0.841463
338 NMN AMP PO4 0.401639 0.8375
339 DCA 0.4 0.837209
340 ETB 0.4 0.825581
341 FNK 0.4 0.797753
342 3D1 0.4 0.789474
343 3L1 0.4 0.789474
344 VRT 0.4 0.7625
345 SO8 0.4 0.759494
Ligand no: 2; Ligand: 51G; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 51G 1 1
2 LLL 0.679012 0.892857
3 GET 0.586207 0.943396
4 827 0.563218 0.890909
5 SIS 0.545455 0.844828
6 DVM 0.423077 0.806452
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CFT; Ligand: APC; Similar sites found with APoc: 67
This union binding pocket(no: 1) in the query (biounit: 5cft.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 4V1F BQ1 None
2 5N8V KZZ None
3 3LRE ADP 1.08108
4 2RNF UM3 1.66667
5 6BR8 6OU 2.16216
6 3PNA CMP 2.5974
7 1FUR MLT 2.7027
8 5UC4 83S 2.7027
9 4FJU NAI 2.7027
10 1YC4 43P 2.7027
11 4E28 9MZ 2.7027
12 5IUY BOG 2.7027
13 4URN NOV 2.7027
14 1DTL BEP 3.10559
15 4Q0A 4OA 3.24324
16 4RW3 PLM 3.24324
17 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.24324
18 5J32 IPM 3.24324
19 1HBK MYR 3.37079
20 1WS5 MMA 3.7594
21 4LSJ LSJ 3.78378
22 2Q0D ATP 3.78378
23 2BHW XAT 4.32432
24 2BHW NEX 4.32432
25 4TV1 36M 4.32432
26 3KP6 SAL 4.63576
27 5C79 PBU 4.66667
28 4DE3 DN8 4.86486
29 1KAH HIS 4.86486
30 1NF8 BOG 4.86486
31 3UYW TAU 4.86486
32 6CB2 OLC 5.11945
33 1N4K I3P 5.40541
34 2HHP FLC 5.40541
35 2OUA AES 5.40541
36 2AF6 BRU 5.40541
37 5C1M OLC 5.6
38 3RV5 DXC 5.61798
39 4O4Z N2O 5.84416
40 3NB0 G6P 5.94595
41 5N26 CPT 6.04396
42 1Q79 3AT 6.48649
43 3AQT RCO 6.48649
44 3FAL REA 6.48649
45 6EWZ GTP 7.02703
46 3KPE TM3 7.69231
47 5U97 PIT 8.10811
48 1BRW URA 8.64865
49 1TV5 N8E 9.18919
50 2D5X L35 9.58904
51 5F5N 5VD 9.72973
52 5L6G XYP 9.72973
53 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 10
54 5CX6 CDP 10.2703
55 5WXU FLC 10.2703
56 4I2D APC 10.2703
57 4A7W GTP 10.8108
58 5LX9 OLB 11.6197
59 5LXT GDP 12.4324
60 3ER9 3AT 13.5135
61 2CIX CEJ 13.5135
62 5I8F ML1 13.9394
63 4LHD GLY 14.5946
64 3E70 GDP 17.2973
65 5ZQ4 AMP 20.5128
66 2WOR 2AN 27
67 4OGQ 7PH 27.027
Pocket No.: 2; Query (leader) PDB : 5CFT; Ligand: 51G; Similar sites found with APoc: 75
This union binding pocket(no: 2) in the query (biounit: 5cft.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4V1F BQ1 None
2 5N8V KZZ None
3 4RYV ZEA None
4 3LRE ADP 1.08108
5 6D28 NEC 1.0989
6 6BR8 6OU 2.16216
7 3PNA CMP 2.5974
8 1FUR MLT 2.7027
9 5UC4 83S 2.7027
10 1YC4 43P 2.7027
11 4E28 9MZ 2.7027
12 5IUY BOG 2.7027
13 4URN NOV 2.7027
14 1DTL BEP 3.10559
15 4Q0A 4OA 3.24324
16 1OGO BGC GLC 3.24324
17 4RW3 PLM 3.24324
18 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.24324
19 5W0N UPU 3.24324
20 1HBK MYR 3.37079
21 5WUU 7UU 3.59712
22 1WS5 MMA 3.7594
23 4LSJ LSJ 3.78378
24 2Q0D ATP 3.78378
25 1EXF GLY 3.78378
26 2BHW XAT 4.32432
27 2BHW NEX 4.32432
28 4TV1 36M 4.32432
29 3KP6 SAL 4.63576
30 5C79 PBU 4.66667
31 4ZNO SUC 4.86486
32 4DE3 DN8 4.86486
33 1KAH HIS 4.86486
34 1NF8 BOG 4.86486
35 3UYW TAU 4.86486
36 3NV3 GAL NAG MAN 5.07246
37 6CB2 OLC 5.11945
38 1N4K I3P 5.40541
39 2HHP FLC 5.40541
40 2OUA AES 5.40541
41 2AF6 BRU 5.40541
42 5C1M OLC 5.6
43 3RV5 DXC 5.61798
44 3NB0 G6P 5.94595
45 3MPB FRU 5.94595
46 5N26 CPT 6.04396
47 1Q79 3AT 6.48649
48 3FAL REA 6.48649
49 3AQT RCO 6.48649
50 3KPE TM3 7.69231
51 4U03 TLL 8.10811
52 4U03 GTP 8.10811
53 5U97 PIT 8.10811
54 1BRW URA 8.64865
55 5DG2 GAL GLC 8.88889
56 4UYG 73B 8.9172
57 1TV5 N8E 9.18919
58 3O6M PRO LYS LEU GLU PRO TRP LYS HIS PRO 9.18919
59 2YMZ LAT 9.23077
60 2D5X L35 9.58904
61 5CX6 CDP 10.2703
62 5WXU FLC 10.2703
63 4I2D APC 10.2703
64 4A7W GTP 10.8108
65 5LX9 OLB 11.6197
66 5LXT GDP 12.4324
67 3BJE URA 12.4324
68 3ER9 3AT 13.5135
69 2CIX CEJ 13.5135
70 5I8F ML1 13.9394
71 4LHD GLY 14.5946
72 3E70 GDP 17.2973
73 5ZQ4 AMP 20.5128
74 2WOR 2AN 27
75 4OGQ 7PH 27.027
APoc FAQ
Feedback