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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 293 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 250 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 204 families.
1 4OXI - GAP C12 H17 N6 O8 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GAP; Similar ligands found: 317
No: Ligand ECFP6 Tc MDL keys Tc
1 GAP 1 1
2 DAL AMP 0.77381 0.958904
3 MYR AMP 0.733333 0.864198
4 ADP PO3 0.710843 0.944444
5 A 0.701299 0.891892
6 AMP 0.701299 0.891892
7 ADP ALF 0.697674 0.871795
8 ALF ADP 0.697674 0.871795
9 CA0 0.695122 0.92
10 ADP VO4 0.689655 0.906667
11 VO4 ADP 0.689655 0.906667
12 TYR AMP 0.684211 0.921053
13 LPA AMP 0.683673 0.864198
14 A12 0.679012 0.858974
15 AP2 0.679012 0.858974
16 ABM 0.675 0.868421
17 A2D 0.675 0.893333
18 ADP 0.670732 0.893333
19 ARG AMP 0.670103 0.9
20 BA3 0.658537 0.893333
21 AP5 0.650602 0.893333
22 B4P 0.650602 0.893333
23 SRA 0.65 0.846154
24 5AL 0.647727 0.932432
25 50T 0.647059 0.857143
26 AN2 0.642857 0.881579
27 SON 0.642857 0.907895
28 AT4 0.642857 0.858974
29 APC 0.639535 0.858974
30 M33 0.635294 0.881579
31 ADX 0.635294 0.807229
32 AU1 0.635294 0.87013
33 SRP 0.633333 0.933333
34 ADV 0.632184 0.883117
35 RBY 0.632184 0.883117
36 ACP 0.627907 0.87013
37 ATP 0.627907 0.893333
38 HEJ 0.627907 0.893333
39 ADP BMA 0.62766 0.945946
40 PAJ 0.623656 0.886076
41 4AD 0.623656 0.921053
42 A A 0.621053 0.893333
43 AR6 0.62069 0.918919
44 PRX 0.62069 0.846154
45 APR 0.62069 0.918919
46 AQP 0.62069 0.893333
47 5FA 0.62069 0.893333
48 DLL 0.617021 0.932432
49 AGS 0.613636 0.848101
50 SAP 0.613636 0.848101
51 AD9 0.613636 0.87013
52 OOB 0.612903 0.932432
53 9ZD 0.612903 0.884615
54 9ZA 0.612903 0.884615
55 8QN 0.612903 0.932432
56 ATP A A A 0.612245 0.931507
57 AMO 0.606383 0.907895
58 WAQ 0.604167 0.884615
59 ACQ 0.6 0.87013
60 ANP 0.6 0.87013
61 TAT 0.6 0.858974
62 00A 0.6 0.884615
63 T99 0.6 0.858974
64 1ZZ 0.597938 0.841463
65 ME8 0.597938 0.841463
66 PTJ 0.597938 0.873418
67 LMS 0.597561 0.785714
68 AMP NAD 0.59633 0.958904
69 3UK 0.59375 0.92
70 OAD 0.59375 0.92
71 AHZ 0.592233 0.864198
72 PR8 0.587629 0.898734
73 LAD 0.587629 0.910256
74 B5V 0.587629 0.907895
75 ATF 0.586957 0.858974
76 9SN 0.585859 0.873418
77 AMP DBH 0.584158 0.894737
78 AHX 0.583333 0.873418
79 NB8 0.581633 0.873418
80 TXA 0.581633 0.907895
81 6YZ 0.580645 0.87013
82 5SV 0.578947 0.804878
83 9X8 0.57732 0.871795
84 AF3 ADP 3PG 0.575472 0.886076
85 AR6 AR6 0.572816 0.945205
86 G5A 0.571429 0.802326
87 4UV 0.568627 0.896104
88 MAP 0.568421 0.848101
89 A22 0.568421 0.881579
90 XYA 0.565789 0.821918
91 ADN 0.565789 0.821918
92 RAB 0.565789 0.821918
93 3OD 0.565657 0.92
94 AOC 0.564706 0.8
95 B5M 0.564356 0.896104
96 B5Y 0.564356 0.896104
97 FA5 0.564356 0.907895
98 YAP 0.564356 0.896104
99 5CD 0.564103 0.783784
100 25A 0.5625 0.893333
101 LAQ 0.561905 0.841463
102 4UU 0.557692 0.896104
103 5AS 0.556818 0.781609
104 A1R 0.556701 0.884615
105 A3R 0.556701 0.884615
106 ADQ 0.556701 0.92
107 NAD 0.553571 0.932432
108 5N5 0.551282 0.821918
109 A4D 0.544304 0.797297
110 A3D 0.54386 0.92
111 XAH 0.543689 0.864198
112 TAD 0.537736 0.839506
113 NXX 0.537037 0.933333
114 DND 0.537037 0.933333
115 4UW 0.537037 0.8625
116 A5A 0.536842 0.788235
117 DTA 0.536585 0.766234
118 TSB 0.536082 0.77907
119 FYA 0.534653 0.857143
120 JB6 0.534653 0.8375
121 BIS 0.534653 0.8375
122 SSA 0.53125 0.781609
123 25L 0.529412 0.881579
124 7MD 0.528302 0.8875
125 A3P 0.52809 0.891892
126 YLP 0.527778 0.865854
127 G A A A 0.526316 0.897436
128 A G 0.526316 0.884615
129 NAJ PZO 0.525862 0.873418
130 U A 0.525862 0.884615
131 54H 0.525773 0.770115
132 VMS 0.525773 0.770115
133 52H 0.525773 0.761364
134 NSS 0.525253 0.781609
135 EP4 0.52439 0.75641
136 DQV 0.523364 0.906667
137 U A G G 0.521739 0.884615
138 53H 0.520408 0.761364
139 5CA 0.520408 0.781609
140 8X1 0.520408 0.775281
141 NVA LMS 0.52 0.755556
142 OMR 0.518182 0.831325
143 TYM 0.518182 0.907895
144 M2T 0.518072 0.7375
145 IOT 0.517857 0.855422
146 3DH 0.517647 0.753247
147 6RE 0.517241 0.78481
148 A A A 0.514852 0.906667
149 LEU LMS 0.514852 0.755556
150 48N 0.513761 0.873418
151 YLB 0.513514 0.865854
152 YLC 0.513514 0.8875
153 4TA 0.513043 0.831325
154 NAE 0.512605 0.896104
155 MTA 0.511905 0.753247
156 PAP 0.510638 0.88
157 LSS 0.51 0.744444
158 DSZ 0.51 0.781609
159 P5A 0.509804 0.766667
160 NAX 0.509091 0.829268
161 6V0 0.509091 0.873418
162 NAI 0.509091 0.860759
163 TXD 0.509091 0.884615
164 NAJ PYZ 0.508333 0.831325
165 NAQ 0.508333 0.873418
166 7D5 0.505882 0.831169
167 J7C 0.505618 0.772152
168 5X8 0.505376 0.789474
169 SFG 0.505376 0.776316
170 9K8 0.504854 0.736264
171 G3A 0.504673 0.85
172 TXE 0.504505 0.884615
173 F2R 0.504348 0.865854
174 ZID 0.504132 0.92
175 GA7 0.5 0.858974
176 G5P 0.5 0.85
177 PO4 PO4 A A A A PO4 0.5 0.90411
178 7MC 0.5 0.865854
179 AFH 0.5 0.8625
180 YLA 0.5 0.865854
181 BT5 0.495726 0.811765
182 CNA 0.495652 0.907895
183 AYB 0.495652 0.855422
184 A4P 0.495575 0.823529
185 GTA 0.495413 0.841463
186 GSU 0.495146 0.781609
187 KAA 0.495146 0.775281
188 A2P 0.494505 0.878378
189 3AM 0.494253 0.878378
190 M24 0.491667 0.851852
191 SAH 0.489583 0.769231
192 A3N 0.488889 0.789474
193 IMO 0.488889 0.853333
194 ZAS 0.488636 0.792208
195 COD 0.487179 0.813953
196 YSA 0.485981 0.761364
197 SMM 0.484848 0.729412
198 SAM 0.484536 0.73494
199 NDC 0.484375 0.873418
200 2A5 0.484211 0.846154
201 S4M 0.483516 0.709302
202 GJV 0.483516 0.775
203 7D3 0.483516 0.833333
204 DZD 0.483051 0.8625
205 UP5 0.482143 0.871795
206 NDE 0.480315 0.907895
207 PPS 0.479592 0.785714
208 SA8 0.479167 0.753086
209 ATR 0.479167 0.866667
210 MAO 0.478261 0.741176
211 A3G 0.477778 0.826667
212 DSH 0.477778 0.75
213 8PZ 0.476636 0.761364
214 Z5A 0.475806 0.802326
215 U A C C 0.475 0.884615
216 A C A C 0.475 0.897436
217 SAI 0.474227 0.759494
218 139 0.474138 0.851852
219 T5A 0.474138 0.8
220 UPA 0.473684 0.884615
221 AP0 0.473684 0.82716
222 4TC 0.473684 0.85
223 GEK 0.470588 0.78481
224 A U 0.469565 0.921053
225 V3L 0.469388 0.918919
226 4YB 0.468468 0.764045
227 N0B 0.467742 0.865854
228 YLY 0.467213 0.855422
229 80F 0.466667 0.821429
230 2AM 0.465909 0.866667
231 EEM 0.464646 0.73494
232 7C5 0.463636 0.820513
233 7D4 0.463158 0.833333
234 N01 0.46281 0.932432
235 5AD 0.4625 0.726027
236 BTX 0.462185 0.8
237 ADJ 0.461538 0.831325
238 NEC 0.461538 0.773333
239 AV2 0.46 0.820513
240 S7M 0.455446 0.73494
241 C2R 0.454545 0.855263
242 A3S 0.452632 0.813333
243 A7D 0.452632 0.779221
244 WSA 0.452174 0.770115
245 A2R 0.45098 0.906667
246 OVE 0.450549 0.833333
247 6AD 0.45 0.817073
248 NMN AMP PO4 0.45 0.896104
249 A5D 0.44898 0.766234
250 U A A U 0.448819 0.884615
251 MHZ 0.447917 0.701149
252 ITT 0.447917 0.842105
253 2SA 0.445545 0.883117
254 A3T 0.443299 0.824324
255 A U C C 0.442748 0.897436
256 Y3J 0.440476 0.706667
257 649 0.439655 0.728261
258 7D7 0.439024 0.746667
259 AMZ 0.438202 0.842105
260 0UM 0.438095 0.765432
261 EAD 0.4375 0.829268
262 8Q2 0.435897 0.736264
263 AAT 0.435644 0.731707
264 P1H 0.435115 0.809524
265 62X 0.433962 0.709302
266 ARU 0.433962 0.795181
267 NAP 0.433071 0.92
268 71V 0.431579 0.814815
269 HFD 0.43 0.848101
270 6C6 0.43 0.8125
271 K15 0.429907 0.72619
272 A6D 0.429907 0.72619
273 DAT 0.428571 0.810127
274 NIA 0.428571 0.780488
275 APC G U 0.427419 0.8375
276 NA0 0.426357 0.907895
277 NHD 0.42623 0.906667
278 6IA 0.425743 0.817073
279 SXZ 0.422018 0.73494
280 NAJ 0.421488 0.932432
281 NVA 2AD 0.42 0.78481
282 TAP 0.418605 0.860759
283 PGS 0.418367 0.814815
284 KB1 0.418182 0.743902
285 NJP 0.418033 0.896104
286 FB0 0.41791 0.786517
287 NA7 0.416667 0.858974
288 6K6 0.415094 0.905405
289 D5M 0.414894 0.807692
290 DA 0.414894 0.807692
291 0WD 0.414634 0.85
292 2VA 0.414141 0.802632
293 ENQ 0.412844 0.917808
294 3NZ 0.412844 0.78481
295 DTP 0.411765 0.810127
296 3AT 0.411765 0.868421
297 AAM 0.410526 0.891892
298 NZQ 0.409836 0.839506
299 CNV FAD 0.409722 0.823529
300 NFD 0.408 0.884615
301 FAD NBT 0.406897 0.752688
302 8BR 0.40625 0.835443
303 D3Y 0.40566 0.792208
304 GGZ 0.40566 0.761905
305 TM1 0.405405 0.755814
306 SLU 0.404762 0.752809
307 A G U U 0.404255 0.864198
308 9JJ 0.40411 0.841463
309 P33 FDA 0.402685 0.788889
310 3AD 0.402299 0.808219
311 VRT 0.401961 0.772152
312 SO8 0.401961 0.792208
313 S8M 0.401869 0.719512
314 AVV 0.401869 0.82716
315 DCA 0.401575 0.804598
316 ETB 0.401575 0.813953
317 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: 85
This union binding pocket(no: 1) in the query (biounit: 4oxi.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5C2N NAG None
2 3A23 GAL 0.868056
3 3KIF GDL 1.88679
4 1F9V ADP 2.30548
5 3LTW HLZ 2.5
6 5WXU FLC 2.50522
7 2J5B TYE 2.58621
8 4OEV OXL 2.63158
9 2G50 ALA 2.83019
10 3BJE R1P 2.86533
11 5W5R PYR 2.87081
12 1Q11 TYE 2.95699
13 1FEC FAD 3.06122
14 2XHK AKG 3.15315
15 1MLD CIT 3.18471
16 6BSW UDP 3.25444
17 4GK9 MAN BMA MAN MAN MAN 3.58423
18 1GQ2 OXL 3.78378
19 4B2G V1N 3.81944
20 4EPM AMP 3.81944
21 3QPB R1P 3.90071
22 2G7C GLA GAL NAG 3.92157
23 5KOD AMP 3.99306
24 5FPE 3TR 4.65116
25 5HM3 649 4.6875
26 4RHS SIA SIA GAL 4.91803
27 1TL2 NDG 5.08475
28 3F5A SIA GAL NAG 5.69106
29 4B2D SER 5.83942
30 2BVE PH5 5.88235
31 1KQR MNA 6.14525
32 1QKQ MAN 7.04225
33 1I1E DM2 7.29167
34 4ODV GP1 Z9M 7.44186
35 4CS9 AMP 7.93651
36 4V1F BQ1 8.13953
37 3CT5 NAG NAG NAG 8.80503
38 3GCM 5GP 9.7561
39 5MST AMP 9.89583
40 5MST FUM 9.89583
41 5EY9 5SV 10.0694
42 4K30 NLG 11.25
43 1HSL HIS 12.605
44 1MDB AMP DBH 12.8015
45 4NAE 1GP 13.7778
46 2Y4O DLL 14.2212
47 2Q89 6CS 18.677
48 4FUT ATP 21.2724
49 4GXQ ATP 22.5296
50 1ZEI CRS 22.6415
51 1RY2 AMP 26.0417
52 1PG4 COA 26.0417
53 1PG4 PRX 26.0417
54 5OE4 3UK 26.0442
55 1V25 ANP 26.8022
56 4DG8 AMP 27.7778
57 5WM2 SAL 27.8369
58 5WM2 AMP 27.8369
59 2D1S SLU 28.1022
60 4RLQ 3SK 28.5164
61 3CW9 AMP 28.7698
62 3CW9 01A 28.7698
63 5C5H 4YB 29.1391
64 4R0M FA5 29.6875
65 2V7B BEZ 29.8677
66 5MSD AMP 30.9028
67 5MSD BEZ 30.9028
68 5IE3 AMP 31.9066
69 5IE3 OXD 31.9066
70 3IES M24 35.2087
71 3DHV DAL AMP 35.7422
72 3C5E ATP 36.8421
73 3E7W AMP 38.5519
74 1AMU AMP 39.9645
75 3O84 HTJ 40.8088
76 5BSR AMP 41.3284
77 5BSR COA 41.3284
78 5X8G S0N 43.5052
79 5N9X 8QN 43.8563
80 5N9X ATP 43.8563
81 5N9X THR 43.8563
82 5N81 8Q2 44.2623
83 4D57 ARG AMP 44.2708
84 3NYQ MCA 45.9406
85 3NYQ AMP 45.9406
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