Receptor
PDB id Resolution Class Description Source Keywords
4OXI 2.26 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF VIBRIO CHOLERAE ADENYLATION DOMAIN ALME COMPLEX WITH GLYCYL-ADENOSINE-5'-PHOSPHATE VIBRIO CHOLERAE SEROTYPE O1 ADENYLATION DOMAIN GLYCINE ATP GLYCYL-ADENOSINE-5-prime -PHOSPHLIGASE
Ref.: ANTIMICROBIAL PEPTIDE RESISTANCE OF VIBRIO CHOLERAE FROM AN LPS MODIFICATION PATHWAY RELATED TO NONRIBO PEPTIDE SYNTHETASES. ACS CHEM.BIOL. V. 9 2382 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GAP A:601;
Valid;
none;
submit data
404.273 C12 H17 N6 O8 P c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4OXI 2.26 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF VIBRIO CHOLERAE ADENYLATION DOMAIN ALME COMPLEX WITH GLYCYL-ADENOSINE-5'-PHOSPHATE VIBRIO CHOLERAE SEROTYPE O1 ADENYLATION DOMAIN GLYCINE ATP GLYCYL-ADENOSINE-5-prime -PHOSPHLIGASE
Ref.: ANTIMICROBIAL PEPTIDE RESISTANCE OF VIBRIO CHOLERAE FROM AN LPS MODIFICATION PATHWAY RELATED TO NONRIBO PEPTIDE SYNTHETASES. ACS CHEM.BIOL. V. 9 2382 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 4OXI - GAP C12 H17 N6 O8 P c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 4OXI - GAP C12 H17 N6 O8 P c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4OXI - GAP C12 H17 N6 O8 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GAP; Similar ligands found: 340
No: Ligand ECFP6 Tc MDL keys Tc
1 GAP 1 1
2 DAL AMP 0.77381 0.958904
3 ADP MG 0.746835 0.944444
4 MYR AMP 0.733333 0.864198
5 ADP PO3 0.710843 0.944444
6 ATP MG 0.710843 0.944444
7 A 0.701299 0.891892
8 AMP 0.701299 0.891892
9 ALF ADP 0.697674 0.871795
10 ADP ALF 0.697674 0.871795
11 CA0 0.695122 0.92
12 ADP VO4 0.689655 0.906667
13 VO4 ADP 0.689655 0.906667
14 KG4 0.686747 0.92
15 TYR AMP 0.684211 0.921053
16 LPA AMP 0.683673 0.864198
17 A12 0.679012 0.858974
18 AP2 0.679012 0.858974
19 A2D 0.675 0.893333
20 ABM 0.675 0.868421
21 45A 0.675 0.868421
22 ADP 0.670732 0.893333
23 ARG AMP 0.670103 0.9
24 BA3 0.658537 0.893333
25 APC MG 0.651163 0.918919
26 B4P 0.650602 0.893333
27 AP5 0.650602 0.893333
28 SRA 0.65 0.846154
29 8LE 0.647727 0.896104
30 5AL 0.647727 0.932432
31 50T 0.647059 0.857143
32 SON 0.642857 0.907895
33 AT4 0.642857 0.858974
34 AN2 0.642857 0.881579
35 APC 0.639535 0.858974
36 8LQ 0.637363 0.907895
37 AU1 0.635294 0.87013
38 M33 0.635294 0.881579
39 ADX 0.635294 0.807229
40 SRP 0.633333 0.933333
41 8LH 0.633333 0.933333
42 ADV 0.632184 0.883117
43 RBY 0.632184 0.883117
44 ACP 0.627907 0.87013
45 ATP 0.627907 0.893333
46 HEJ 0.627907 0.893333
47 ADP BMA 0.62766 0.945946
48 4AD 0.623656 0.921053
49 PAJ 0.623656 0.886076
50 A A 0.621053 0.893333
51 APR 0.62069 0.918919
52 AQP 0.62069 0.893333
53 AR6 0.62069 0.918919
54 5FA 0.62069 0.893333
55 PRX 0.62069 0.846154
56 DLL 0.617021 0.932432
57 AGS 0.613636 0.848101
58 SAP 0.613636 0.848101
59 AD9 0.613636 0.87013
60 9ZA 0.612903 0.884615
61 8QN 0.612903 0.932432
62 OOB 0.612903 0.932432
63 9ZD 0.612903 0.884615
64 ATP A A A 0.612245 0.931507
65 ATP A 0.612245 0.931507
66 AMO 0.606383 0.907895
67 WAQ 0.604167 0.884615
68 00A 0.6 0.884615
69 T99 0.6 0.858974
70 TAT 0.6 0.858974
71 ACQ 0.6 0.87013
72 ANP 0.6 0.87013
73 1ZZ 0.597938 0.841463
74 ME8 0.597938 0.841463
75 PTJ 0.597938 0.873418
76 LMS 0.597561 0.785714
77 AMP NAD 0.59633 0.958904
78 OAD 0.59375 0.92
79 3UK 0.59375 0.92
80 AHZ 0.592233 0.864198
81 PR8 0.587629 0.898734
82 LAD 0.587629 0.910256
83 B5V 0.587629 0.907895
84 ATF 0.586957 0.858974
85 9SN 0.585859 0.873418
86 AMP DBH 0.584158 0.894737
87 AHX 0.583333 0.873418
88 NB8 0.581633 0.873418
89 TXA 0.581633 0.907895
90 6YZ 0.580645 0.87013
91 5SV 0.578947 0.804878
92 9X8 0.57732 0.871795
93 AF3 ADP 3PG 0.575472 0.886076
94 HQG 0.574468 0.906667
95 AR6 AR6 0.572816 0.945205
96 G5A 0.571429 0.802326
97 4UV 0.568627 0.896104
98 MAP 0.568421 0.848101
99 A22 0.568421 0.881579
100 RAB 0.565789 0.821918
101 ADN 0.565789 0.821918
102 XYA 0.565789 0.821918
103 3OD 0.565657 0.92
104 AOC 0.564706 0.8
105 YAP 0.564356 0.896104
106 FA5 0.564356 0.907895
107 B5Y 0.564356 0.896104
108 B5M 0.564356 0.896104
109 5CD 0.564103 0.783784
110 OZV 0.5625 0.893333
111 25A 0.5625 0.893333
112 LAQ 0.561905 0.841463
113 4UU 0.557692 0.896104
114 5AS 0.556818 0.781609
115 A1R 0.556701 0.884615
116 ADQ 0.556701 0.92
117 A3R 0.556701 0.884615
118 NAD 0.553571 0.932432
119 5N5 0.551282 0.821918
120 A4D 0.544304 0.797297
121 A3D 0.54386 0.92
122 XAH 0.543689 0.864198
123 H1Q 0.538462 0.88
124 TAD 0.537736 0.839506
125 NXX 0.537037 0.933333
126 4UW 0.537037 0.8625
127 DND 0.537037 0.933333
128 A5A 0.536842 0.788235
129 DTA 0.536585 0.766234
130 TSB 0.536082 0.77907
131 JB6 0.534653 0.8375
132 BIS 0.534653 0.8375
133 FYA 0.534653 0.857143
134 SSA 0.53125 0.781609
135 25L 0.529412 0.881579
136 7MD 0.528302 0.8875
137 A3P 0.52809 0.891892
138 YLP 0.527778 0.865854
139 G A A A 0.526316 0.897436
140 A G 0.526316 0.884615
141 U A 0.525862 0.884615
142 NAJ PZO 0.525862 0.873418
143 52H 0.525773 0.761364
144 VMS 0.525773 0.770115
145 54H 0.525773 0.770115
146 NSS 0.525253 0.781609
147 EP4 0.52439 0.75641
148 DQV 0.523364 0.906667
149 U A G G 0.521739 0.884615
150 53H 0.520408 0.761364
151 8X1 0.520408 0.775281
152 5CA 0.520408 0.781609
153 NVA LMS 0.52 0.755556
154 OMR 0.518182 0.831325
155 TYM 0.518182 0.907895
156 M2T 0.518072 0.7375
157 IOT 0.517857 0.855422
158 3DH 0.517647 0.753247
159 6RE 0.517241 0.78481
160 LEU LMS 0.514852 0.755556
161 A A A 0.514852 0.906667
162 48N 0.513761 0.873418
163 YLC 0.513514 0.8875
164 YLB 0.513514 0.865854
165 4TA 0.513043 0.831325
166 NAE 0.512605 0.896104
167 MTA 0.511905 0.753247
168 PAP 0.510638 0.88
169 LSS 0.51 0.744444
170 DSZ 0.51 0.781609
171 P5A 0.509804 0.766667
172 NAI 0.509091 0.860759
173 6V0 0.509091 0.873418
174 NAX 0.509091 0.829268
175 TXD 0.509091 0.884615
176 NAQ 0.508333 0.873418
177 NAJ PYZ 0.508333 0.831325
178 7D5 0.505882 0.831169
179 J7C 0.505618 0.772152
180 5X8 0.505376 0.789474
181 SFG 0.505376 0.776316
182 9K8 0.504854 0.736264
183 G3A 0.504673 0.85
184 TXE 0.504505 0.884615
185 F2R 0.504348 0.865854
186 ZID 0.504132 0.92
187 AFH 0.5 0.8625
188 7MC 0.5 0.865854
189 G5P 0.5 0.85
190 GA7 0.5 0.858974
191 PO4 PO4 A A A A PO4 0.5 0.90411
192 YLA 0.5 0.865854
193 BT5 0.495726 0.811765
194 CNA 0.495652 0.907895
195 AYB 0.495652 0.855422
196 A4P 0.495575 0.823529
197 GTA 0.495413 0.841463
198 GSU 0.495146 0.781609
199 KAA 0.495146 0.775281
200 A2P 0.494505 0.878378
201 3AM 0.494253 0.878378
202 M24 0.491667 0.851852
203 SAH 0.489583 0.769231
204 A3N 0.488889 0.789474
205 IMO 0.488889 0.853333
206 ZAS 0.488636 0.792208
207 COD 0.487179 0.813953
208 B1U 0.485981 0.73913
209 YSA 0.485981 0.761364
210 SMM 0.484848 0.729412
211 SAM 0.484536 0.73494
212 NDC 0.484375 0.873418
213 2A5 0.484211 0.846154
214 7D3 0.483516 0.833333
215 GJV 0.483516 0.775
216 S4M 0.483516 0.709302
217 DZD 0.483051 0.8625
218 UP5 0.482143 0.871795
219 NDE 0.480315 0.907895
220 PPS 0.479592 0.785714
221 SA8 0.479167 0.753086
222 ATR 0.479167 0.866667
223 MAO 0.478261 0.741176
224 A3G 0.477778 0.826667
225 DSH 0.477778 0.75
226 8PZ 0.476636 0.761364
227 Z5A 0.475806 0.802326
228 A C A C 0.475 0.897436
229 U A C C 0.475 0.884615
230 SAI 0.474227 0.759494
231 T5A 0.474138 0.8
232 139 0.474138 0.851852
233 4TC 0.473684 0.85
234 UPA 0.473684 0.884615
235 AP0 0.473684 0.82716
236 GEK 0.470588 0.78481
237 A U 0.469565 0.921053
238 V3L 0.469388 0.918919
239 4YB 0.468468 0.764045
240 N0B 0.467742 0.865854
241 6MZ 0.467391 0.855263
242 YLY 0.467213 0.855422
243 80F 0.466667 0.821429
244 2AM 0.465909 0.866667
245 EEM 0.464646 0.73494
246 7C5 0.463636 0.820513
247 7D4 0.463158 0.833333
248 N01 0.46281 0.932432
249 5AD 0.4625 0.726027
250 BTX 0.462185 0.8
251 ADJ 0.461538 0.831325
252 NEC 0.461538 0.773333
253 KOY 0.460177 0.828947
254 AV2 0.46 0.820513
255 S7M 0.455446 0.73494
256 C2R 0.454545 0.855263
257 J4G 0.45283 0.896104
258 A3S 0.452632 0.813333
259 A7D 0.452632 0.779221
260 WSA 0.452174 0.770115
261 N5A 0.451613 0.763158
262 A2R 0.45098 0.906667
263 OVE 0.450549 0.833333
264 6AD 0.45 0.817073
265 NMN AMP PO4 0.45 0.896104
266 A5D 0.44898 0.766234
267 U A A U 0.448819 0.884615
268 MHZ 0.447917 0.701149
269 ITT 0.447917 0.842105
270 N5O 0.445652 0.789474
271 2SA 0.445545 0.883117
272 A3T 0.443299 0.824324
273 A U C C 0.442748 0.897436
274 Y3J 0.440476 0.706667
275 649 0.439655 0.728261
276 7D7 0.439024 0.746667
277 AMZ 0.438202 0.842105
278 0UM 0.438095 0.765432
279 EAD 0.4375 0.829268
280 COA FLC 0.436508 0.835294
281 8Q2 0.435897 0.736264
282 AAT 0.435644 0.731707
283 P1H 0.435115 0.809524
284 62X 0.433962 0.709302
285 ARU 0.433962 0.795181
286 NAP 0.433071 0.92
287 71V 0.431579 0.814815
288 HFD 0.43 0.848101
289 JSQ 0.43 0.848101
290 6C6 0.43 0.8125
291 K15 0.429907 0.72619
292 A6D 0.429907 0.72619
293 DAT 0.428571 0.810127
294 NIA 0.428571 0.780488
295 APC G U 0.427419 0.8375
296 NA0 0.426357 0.907895
297 NHD 0.42623 0.906667
298 6IA 0.425743 0.817073
299 NO7 0.423077 0.883117
300 SXZ 0.422018 0.73494
301 NAJ 0.421488 0.932432
302 NVA 2AD 0.42 0.78481
303 TAP 0.418605 0.860759
304 PGS 0.418367 0.814815
305 KB1 0.418182 0.743902
306 NJP 0.418033 0.896104
307 FB0 0.41791 0.786517
308 NA7 0.416667 0.858974
309 6K6 0.415094 0.905405
310 DA 0.414894 0.807692
311 D5M 0.414894 0.807692
312 0WD 0.414634 0.85
313 2VA 0.414141 0.802632
314 ENQ 0.412844 0.917808
315 3NZ 0.412844 0.78481
316 DTP 0.411765 0.810127
317 3AT 0.411765 0.868421
318 AAM 0.410526 0.891892
319 NZQ 0.409836 0.839506
320 CNV FAD 0.409722 0.823529
321 NFD 0.408 0.884615
322 LQJ 0.40708 0.893333
323 FAD NBT 0.406897 0.752688
324 8BR 0.40625 0.835443
325 D3Y 0.40566 0.792208
326 GGZ 0.40566 0.761905
327 TM1 0.405405 0.755814
328 SLU 0.404762 0.752809
329 A G U U 0.404255 0.864198
330 9JJ 0.40411 0.841463
331 N37 0.403361 0.759494
332 P33 FDA 0.402685 0.788889
333 3AD 0.402299 0.808219
334 VRT 0.401961 0.772152
335 SO8 0.401961 0.792208
336 S8M 0.401869 0.719512
337 AVV 0.401869 0.82716
338 ETB 0.401575 0.813953
339 DCA 0.401575 0.804598
340 ALF 5GP 0.4 0.819277
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OXI; Ligand: GAP; Similar sites found with APoc: 9
This union binding pocket(no: 1) in the query (biounit: 4oxi.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5MST AMP 9.89583
2 1RY2 AMP 26.0417
3 4DG8 AMP 27.7778
4 3DHV DAL AMP 35.7422
5 6IJB AMP 37.1058
6 3E7W AMP 38.5519
7 1AMU AMP 39.9645
8 1AMU AMP 39.9645
9 6AKD A5A 44.4238
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