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 319 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 271 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 223 families.
1 4OXI - GAP C12 H17 N6 O8 P c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GAP; Similar ligands found: 364
No: Ligand ECFP6 Tc MDL keys Tc
1 GAP 1 1
2 DAL AMP 0.77381 0.958904
3 ADP BEF 0.746835 0.944444
4 ADP MG 0.746835 0.944444
5 AMP MG 0.736842 0.930556
6 MYR AMP 0.733333 0.864198
7 ATP MG 0.710843 0.944444
8 ADP PO3 0.710843 0.944444
9 BEF ADP 0.702381 0.918919
10 A 0.701299 0.891892
11 AMP 0.701299 0.891892
12 ALF ADP 0.697674 0.871795
13 CA0 0.695122 0.92
14 KG4 0.686747 0.92
15 LPA AMP 0.683673 0.864198
16 AP2 0.679012 0.858974
17 A12 0.679012 0.858974
18 VO4 ADP 0.678161 0.894737
19 ANP MG 0.678161 0.906667
20 ABM 0.675 0.868421
21 A2D 0.675 0.893333
22 45A 0.675 0.868421
23 ADP 0.670732 0.893333
24 ARG AMP 0.670103 0.9
25 BA3 0.658537 0.893333
26 APC MG 0.651163 0.918919
27 AP5 0.650602 0.893333
28 B4P 0.650602 0.893333
29 SRA 0.65 0.846154
30 8LE 0.647727 0.896104
31 5AL 0.647727 0.932432
32 50T 0.647059 0.857143
33 AT4 0.642857 0.858974
34 SON 0.642857 0.907895
35 AN2 0.642857 0.881579
36 APC 0.639535 0.858974
37 8LQ 0.637363 0.907895
38 ADX 0.635294 0.807229
39 AU1 0.635294 0.87013
40 M33 0.635294 0.881579
41 8LH 0.633333 0.933333
42 SRP 0.633333 0.933333
43 ADV 0.632184 0.883117
44 RBY 0.632184 0.883117
45 V2G 0.629214 0.922078
46 ACP 0.627907 0.87013
47 HEJ 0.627907 0.893333
48 ATP 0.627907 0.893333
49 ADP BMA 0.62766 0.945946
50 4AD 0.623656 0.921053
51 PAJ 0.623656 0.886076
52 AR6 0.62069 0.918919
53 PRX 0.62069 0.846154
54 APR 0.62069 0.918919
55 AQP 0.62069 0.893333
56 5FA 0.62069 0.893333
57 QA7 0.619565 0.896104
58 DLL 0.617021 0.932432
59 AD9 0.613636 0.87013
60 AGS 0.613636 0.848101
61 9ZA 0.612903 0.884615
62 8QN 0.612903 0.932432
63 OOB 0.612903 0.932432
64 9ZD 0.612903 0.884615
65 ATP A 0.612245 0.931507
66 ATP A A A 0.612245 0.931507
67 AMO 0.606383 0.907895
68 WAQ 0.604167 0.884615
69 ANP 0.6 0.87013
70 TAT 0.6 0.858974
71 ACQ 0.6 0.87013
72 00A 0.6 0.884615
73 T99 0.6 0.858974
74 PTJ 0.597938 0.873418
75 ME8 0.597938 0.841463
76 1ZZ 0.597938 0.841463
77 LMS 0.597561 0.785714
78 AMP NAD 0.59633 0.958904
79 3UK 0.59375 0.92
80 OAD 0.59375 0.92
81 AHZ 0.592233 0.864198
82 ALF ADP 3PG 0.590476 0.886076
83 B5V 0.587629 0.907895
84 PR8 0.587629 0.898734
85 LAD 0.587629 0.910256
86 ATF 0.586957 0.858974
87 9SN 0.585859 0.873418
88 NAD IBO 0.584906 0.945205
89 NAD TDB 0.584906 0.945205
90 AMP DBH 0.584158 0.894737
91 AHX 0.583333 0.873418
92 TXA 0.581633 0.907895
93 NB8 0.581633 0.873418
94 6YZ 0.580645 0.87013
95 5SV 0.578947 0.804878
96 9X8 0.57732 0.871795
97 AF3 ADP 3PG 0.575472 0.886076
98 HQG 0.574468 0.906667
99 AR6 AR6 0.572816 0.945205
100 G5A 0.571429 0.802326
101 4UV 0.568627 0.896104
102 MAP 0.568421 0.848101
103 A22 0.568421 0.881579
104 ADN 0.565789 0.821918
105 XYA 0.565789 0.821918
106 RAB 0.565789 0.821918
107 3OD 0.565657 0.92
108 AOC 0.564706 0.8
109 FA5 0.564356 0.907895
110 B5M 0.564356 0.896104
111 B5Y 0.564356 0.896104
112 5CD 0.564103 0.783784
113 25A 0.5625 0.893333
114 OZV 0.5625 0.893333
115 LAQ 0.561905 0.841463
116 4UU 0.557692 0.896104
117 5AS 0.556818 0.781609
118 A3R 0.556701 0.884615
119 A1R 0.556701 0.884615
120 ADQ 0.556701 0.92
121 NAD 0.553571 0.932432
122 5N5 0.551282 0.821918
123 JNT 0.55102 0.894737
124 A4D 0.544304 0.797297
125 A3D 0.54386 0.92
126 XAH 0.543689 0.864198
127 H1Q 0.538462 0.88
128 TAD 0.537736 0.839506
129 DND 0.537037 0.933333
130 4UW 0.537037 0.8625
131 A5A 0.536842 0.788235
132 DTA 0.536585 0.766234
133 TSB 0.536082 0.77907
134 BIS 0.534653 0.8375
135 JB6 0.534653 0.8375
136 FYA 0.534653 0.857143
137 SSA 0.53125 0.781609
138 LEU LMS 0.53 0.772727
139 25L 0.529412 0.881579
140 7MD 0.528302 0.8875
141 A3P 0.52809 0.891892
142 YLP 0.527778 0.865854
143 NAJ PZO 0.525862 0.873418
144 52H 0.525773 0.761364
145 54H 0.525773 0.770115
146 VMS 0.525773 0.770115
147 NSS 0.525253 0.781609
148 EP4 0.52439 0.75641
149 DQV 0.523364 0.906667
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 KMQ 0.519231 0.883117
155 TYM 0.518182 0.907895
156 OMR 0.518182 0.831325
157 M2T 0.518072 0.7375
158 IOT 0.517857 0.855422
159 3DH 0.517647 0.753247
160 6RE 0.517241 0.78481
161 48N 0.513761 0.873418
162 YLC 0.513514 0.8875
163 YLB 0.513514 0.865854
164 4TA 0.513043 0.831325
165 NAE 0.512605 0.896104
166 MTA 0.511905 0.753247
167 PAP 0.510638 0.88
168 DSZ 0.51 0.781609
169 LSS 0.51 0.744444
170 P5A 0.509804 0.766667
171 6V0 0.509091 0.873418
172 NAX 0.509091 0.829268
173 NAI 0.509091 0.860759
174 TXD 0.509091 0.884615
175 NAJ PYZ 0.508333 0.831325
176 NAQ 0.508333 0.873418
177 NWW 0.506173 0.739726
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 L3W 0.5 0.883117
188 G5P 0.5 0.85
189 GA7 0.5 0.858974
190 YLA 0.5 0.865854
191 AFH 0.5 0.8625
192 PO4 PO4 A A A A PO4 0.5 0.90411
193 7MC 0.5 0.865854
194 BT5 0.495726 0.811765
195 AYB 0.495652 0.855422
196 CNA 0.495652 0.907895
197 A4P 0.495575 0.823529
198 GTA 0.495413 0.841463
199 GSU 0.495146 0.781609
200 KAA 0.495146 0.775281
201 A2P 0.494505 0.878378
202 3AM 0.494253 0.878378
203 M24 0.491667 0.851852
204 SAH 0.489583 0.769231
205 A3N 0.488889 0.789474
206 IMO 0.488889 0.853333
207 ZAS 0.488636 0.792208
208 COD 0.487179 0.813953
209 B1U 0.485981 0.73913
210 YSA 0.485981 0.761364
211 V47 0.484848 0.810811
212 SMM 0.484848 0.729412
213 SAM 0.484536 0.73494
214 NDC 0.484375 0.873418
215 2A5 0.484211 0.846154
216 GJV 0.483516 0.775
217 7D3 0.483516 0.833333
218 S4M 0.483516 0.709302
219 DZD 0.483051 0.8625
220 UP5 0.482143 0.871795
221 NDE 0.480315 0.907895
222 PPS 0.479592 0.785714
223 SA8 0.479167 0.753086
224 ATR 0.479167 0.866667
225 MAO 0.478261 0.741176
226 DSH 0.477778 0.75
227 A3G 0.477778 0.826667
228 8PZ 0.476636 0.761364
229 Z5A 0.475806 0.802326
230 SAI 0.474227 0.759494
231 O02 0.474227 0.82716
232 139 0.474138 0.851852
233 T5A 0.474138 0.8
234 UPA 0.473684 0.884615
235 AP0 0.473684 0.82716
236 4TC 0.473684 0.85
237 GEK 0.470588 0.78481
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 D4F 0.463415 0.841463
248 7D4 0.463158 0.833333
249 N01 0.46281 0.932432
250 5AD 0.4625 0.726027
251 BTX 0.462185 0.8
252 ADJ 0.461538 0.831325
253 NEC 0.461538 0.773333
254 KOY 0.460177 0.828947
255 AV2 0.46 0.820513
256 NAD BBN 0.459259 0.821429
257 QXG 0.457143 0.758621
258 QXP 0.456311 0.767442
259 S7M 0.455446 0.73494
260 C2R 0.454545 0.855263
261 J4G 0.45283 0.896104
262 A7D 0.452632 0.779221
263 A3S 0.452632 0.813333
264 NAD CJ3 0.452555 0.793103
265 WSA 0.452174 0.770115
266 N5A 0.451613 0.763158
267 A2R 0.45098 0.906667
268 OVE 0.450549 0.833333
269 NMN AMP PO4 0.45 0.896104
270 6AD 0.45 0.817073
271 K3K 0.449541 0.782051
272 NWQ 0.449438 0.72
273 A5D 0.44898 0.766234
274 MHZ 0.447917 0.701149
275 ITT 0.447917 0.842105
276 N5O 0.445652 0.789474
277 2SA 0.445545 0.883117
278 A3T 0.443299 0.824324
279 K3E 0.441441 0.794872
280 Y3J 0.440476 0.706667
281 649 0.439655 0.728261
282 R2V 0.439252 0.767442
283 7D7 0.439024 0.746667
284 AMZ 0.438202 0.842105
285 0UM 0.438095 0.765432
286 EAD 0.4375 0.829268
287 COA FLC 0.436508 0.835294
288 8Q2 0.435897 0.736264
289 AAT 0.435644 0.731707
290 P1H 0.435115 0.809524
291 ARU 0.433962 0.795181
292 62X 0.433962 0.709302
293 NAP 0.433071 0.92
294 71V 0.431579 0.814815
295 JSQ 0.43 0.848101
296 HFD 0.43 0.848101
297 6C6 0.43 0.8125
298 K15 0.429907 0.72619
299 A6D 0.429907 0.72619
300 DAT 0.428571 0.810127
301 NIA 0.428571 0.780488
302 CUU 0.428571 0.868421
303 NA0 0.426357 0.907895
304 NHD 0.42623 0.906667
305 6IA 0.425743 0.817073
306 NAD NDT 0.424658 0.71134
307 NO7 0.423077 0.883117
308 SXZ 0.422018 0.73494
309 38V 0.421875 0.819277
310 NAJ 0.421488 0.932432
311 K2H 0.420561 0.7375
312 NVA 2AD 0.42 0.78481
313 CNV FAD 0.41958 0.795455
314 KY2 0.419048 0.73494
315 DAL FAD PER 0.418919 0.788889
316 TAP 0.418605 0.860759
317 PGS 0.418367 0.814815
318 KB1 0.418182 0.743902
319 NJP 0.418033 0.896104
320 FB0 0.41791 0.786517
321 NA7 0.416667 0.858974
322 PLP AAD 0.416 0.736264
323 6K6 0.415094 0.905405
324 D5M 0.414894 0.807692
325 DA 0.414894 0.807692
326 0WD 0.414634 0.85
327 2VA 0.414141 0.802632
328 K2K 0.412844 0.740741
329 ENQ 0.412844 0.917808
330 3NZ 0.412844 0.78481
331 DTP 0.411765 0.810127
332 NX8 0.411765 0.740741
333 3AT 0.411765 0.868421
334 KYB 0.411215 0.73494
335 AAM 0.410526 0.891892
336 NZQ 0.409836 0.839506
337 O05 0.409091 0.823529
338 K2R 0.409091 0.857143
339 NFD 0.408 0.884615
340 NDP DTT 0.407407 0.843373
341 LQJ 0.40708 0.893333
342 KYE 0.40708 0.759036
343 FAD NBT 0.406897 0.752688
344 EU9 0.40678 0.727273
345 8BR 0.40625 0.835443
346 APC G U 0.40625 0.8375
347 D3Y 0.40566 0.792208
348 GGZ 0.40566 0.761905
349 TM1 0.405405 0.755814
350 SLU 0.404762 0.752809
351 9JJ 0.40411 0.841463
352 FAD T2C 0.403974 0.791209
353 N37 0.403361 0.759494
354 P33 FDA 0.402685 0.788889
355 3AD 0.402299 0.808219
356 VRT 0.401961 0.772152
357 SO8 0.401961 0.792208
358 AVV 0.401869 0.82716
359 S8M 0.401869 0.719512
360 K38 0.401786 0.782051
361 DCA 0.401575 0.804598
362 ETB 0.401575 0.813953
363 BUA COA 0.40146 0.816092
364 ALF 5GP 0.4 0.819277
Similar Ligands (3D)
Ligand no: 1; Ligand: GAP; Similar ligands found: 11
No: Ligand Similarity coefficient
1 GDP 0.9328
2 IDP 0.9225
3 UDP 0.8984
4 GNH 0.8875
5 GDP MG 0.8874
6 M7G 0.8824
7 5GP 0.8768
8 FMP 0.8736
9 IMP 0.8718
10 G 0.8544
11 IMU 0.8541
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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