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 250 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 217 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 181 families.
1 4OXI - GAP C12 H17 N6 O8 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GAP; Similar ligands found: 306
No: Ligand ECFP6 Tc MDL keys Tc
1 GAP 1 1
2 DAL AMP 0.752941 0.958904
3 ADP MG 0.7375 0.906667
4 MYR AMP 0.733333 0.864198
5 BEF ADP 0.728395 0.883117
6 ADP BEF 0.728395 0.883117
7 AMP MG 0.727273 0.893333
8 ADP PO3 0.710843 0.944444
9 ATP MG 0.702381 0.906667
10 AMP 0.701299 0.891892
11 A 0.701299 0.891892
12 ALF ADP 0.697674 0.871795
13 ADP ALF 0.697674 0.871795
14 CA0 0.695122 0.92
15 ADP VO4 0.689655 0.906667
16 VO4 ADP 0.689655 0.906667
17 LPA AMP 0.683673 0.864198
18 A12 0.679012 0.858974
19 AP2 0.679012 0.858974
20 ABM 0.675 0.868421
21 A2D 0.675 0.893333
22 TYR AMP 0.673684 0.933333
23 ADP 0.670732 0.893333
24 ANP MG 0.670455 0.871795
25 BA3 0.658537 0.893333
26 AP5 0.650602 0.893333
27 B4P 0.650602 0.893333
28 SRA 0.65 0.846154
29 5AL 0.647727 0.932432
30 50T 0.647059 0.857143
31 SON 0.642857 0.907895
32 AN2 0.642857 0.881579
33 ARG AMP 0.64 0.9
34 APC 0.639535 0.858974
35 ADX 0.635294 0.807229
36 AU1 0.635294 0.87013
37 M33 0.635294 0.881579
38 SRP 0.633333 0.933333
39 RBY 0.632184 0.883117
40 ADV 0.632184 0.883117
41 ACP 0.627907 0.87013
42 ATP 0.627907 0.893333
43 ADP BMA 0.62766 0.945946
44 PAJ 0.623656 0.886076
45 4AD 0.623656 0.921053
46 A A 0.621053 0.893333
47 AR6 0.62069 0.918919
48 5FA 0.62069 0.893333
49 APR 0.62069 0.918919
50 PRX 0.62069 0.846154
51 AQP 0.62069 0.893333
52 DLL 0.617021 0.932432
53 AGS 0.613636 0.848101
54 SAP 0.613636 0.848101
55 AD9 0.613636 0.87013
56 OOB 0.612903 0.932432
57 8QN 0.612903 0.932432
58 ATP A A A 0.612245 0.931507
59 AMO 0.606383 0.907895
60 WAQ 0.604167 0.884615
61 ACQ 0.6 0.87013
62 ANP 0.6 0.87013
63 00A 0.6 0.884615
64 TAT 0.6 0.858974
65 PTJ 0.597938 0.873418
66 ME8 0.597938 0.841463
67 1ZZ 0.597938 0.841463
68 3UK 0.59375 0.92
69 OAD 0.59375 0.92
70 AHZ 0.592233 0.864198
71 ALF ADP 3PG 0.590476 0.886076
72 LA8 ALF 3PG 0.590476 0.886076
73 LAD 0.587629 0.910256
74 PR8 0.587629 0.898734
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 TXA 0.581633 0.907895
80 NB8 0.581633 0.873418
81 5SV 0.578947 0.804878
82 AF3 ADP 3PG 0.575472 0.886076
83 AR6 AR6 0.572816 0.945205
84 G5A 0.571429 0.802326
85 4UV 0.568627 0.896104
86 A22 0.568421 0.881579
87 MAP 0.568421 0.848101
88 XYA 0.565789 0.821918
89 ADN 0.565789 0.821918
90 RAB 0.565789 0.821918
91 3OD 0.565657 0.92
92 AOC 0.564706 0.8
93 FA5 0.564356 0.907895
94 YAP 0.564356 0.896104
95 5CD 0.564103 0.783784
96 25A 0.5625 0.893333
97 LAQ 0.561905 0.841463
98 NAD IBO 0.558559 0.896104
99 4UU 0.557692 0.896104
100 5AS 0.556818 0.781609
101 ADQ 0.556701 0.92
102 A1R 0.556701 0.884615
103 AMP NAD 0.555556 0.933333
104 NAD 0.553571 0.932432
105 5N5 0.551282 0.821918
106 A4D 0.544304 0.797297
107 A3D 0.54386 0.92
108 XAH 0.543689 0.864198
109 TAD 0.537736 0.839506
110 4UW 0.537037 0.8625
111 DND 0.537037 0.933333
112 NXX 0.537037 0.933333
113 A5A 0.536842 0.788235
114 DTA 0.536585 0.766234
115 TSB 0.536082 0.77907
116 BIS 0.534653 0.8375
117 JB6 0.534653 0.8375
118 FYA 0.534653 0.857143
119 SSA 0.53125 0.781609
120 25L 0.529412 0.881579
121 7MD 0.528302 0.8875
122 A3P 0.52809 0.891892
123 YLP 0.527778 0.865854
124 G A A A 0.526316 0.897436
125 NAJ PZO 0.525862 0.873418
126 VMS 0.525773 0.770115
127 54H 0.525773 0.770115
128 52H 0.525773 0.761364
129 NSS 0.525253 0.781609
130 EP4 0.52439 0.75641
131 U A G G 0.521739 0.884615
132 NAJ PYZ 0.521008 0.851852
133 5CA 0.520408 0.781609
134 53H 0.520408 0.761364
135 OMR 0.518182 0.831325
136 TYM 0.518182 0.907895
137 M2T 0.518072 0.7375
138 IOT 0.517857 0.855422
139 3DH 0.517647 0.753247
140 6RE 0.517241 0.78481
141 A A A 0.514852 0.906667
142 48N 0.513761 0.873418
143 YLB 0.513514 0.865854
144 YLC 0.513514 0.8875
145 4TA 0.513043 0.831325
146 NAE 0.512605 0.896104
147 MTA 0.511905 0.753247
148 PAP 0.510638 0.88
149 DSZ 0.51 0.781609
150 LSS 0.51 0.744444
151 P5A 0.509804 0.766667
152 TXD 0.509091 0.884615
153 NAI 0.509091 0.860759
154 NAX 0.509091 0.829268
155 6V0 0.509091 0.873418
156 NAQ 0.508333 0.873418
157 7D5 0.505882 0.831169
158 J7C 0.505618 0.772152
159 5X8 0.505376 0.789474
160 SFG 0.505376 0.776316
161 NVA LMS 0.504951 0.764045
162 G3A 0.504673 0.85
163 TXE 0.504505 0.884615
164 ZID 0.504132 0.92
165 YLA 0.5 0.865854
166 G5P 0.5 0.85
167 LEU LMS 0.5 0.764045
168 AFH 0.5 0.8625
169 7MC 0.5 0.865854
170 PO4 PO4 A A A A PO4 0.5 0.90411
171 BT5 0.495726 0.811765
172 CNA 0.495652 0.907895
173 AYB 0.495652 0.855422
174 A4P 0.495575 0.823529
175 GTA 0.495413 0.841463
176 KAA 0.495146 0.775281
177 GSU 0.495146 0.781609
178 A2P 0.494505 0.878378
179 3AM 0.494253 0.878378
180 M24 0.491667 0.851852
181 SAH 0.489583 0.769231
182 A3N 0.488889 0.789474
183 IMO 0.488889 0.853333
184 ZAS 0.488636 0.792208
185 COD 0.487179 0.813953
186 YSA 0.485981 0.761364
187 SMM 0.484848 0.729412
188 SAM 0.484536 0.73494
189 NDC 0.484375 0.873418
190 2A5 0.484211 0.846154
191 7D3 0.483516 0.833333
192 GJV 0.483516 0.775
193 S4M 0.483516 0.709302
194 DZD 0.483051 0.8625
195 UP5 0.482143 0.871795
196 NDE 0.480315 0.907895
197 PPS 0.479592 0.785714
198 SA8 0.479167 0.753086
199 ATR 0.479167 0.866667
200 MAO 0.478261 0.741176
201 A3G 0.477778 0.826667
202 DSH 0.477778 0.75
203 Z5A 0.475806 0.802326
204 U A C C 0.475 0.884615
205 SAI 0.474227 0.759494
206 T5A 0.474138 0.8
207 139 0.474138 0.851852
208 UPA 0.473684 0.884615
209 AP0 0.473684 0.82716
210 4TC 0.473684 0.85
211 GEK 0.470588 0.78481
212 U G A 0.469697 0.864198
213 A U 0.469565 0.921053
214 V3L 0.469388 0.918919
215 4YB 0.468468 0.764045
216 N0B 0.467742 0.865854
217 YLY 0.467213 0.855422
218 2AM 0.465909 0.866667
219 EEM 0.464646 0.73494
220 7C5 0.463636 0.820513
221 7D4 0.463158 0.833333
222 N01 0.46281 0.932432
223 5AD 0.4625 0.726027
224 BTX 0.462185 0.8
225 ADJ 0.461538 0.831325
226 NEC 0.461538 0.773333
227 AV2 0.46 0.820513
228 NAD BBN 0.459259 0.821429
229 S7M 0.455446 0.73494
230 C2R 0.454545 0.855263
231 A3S 0.452632 0.813333
232 A7D 0.452632 0.779221
233 NAD CJ3 0.452555 0.793103
234 WSA 0.452174 0.770115
235 A2R 0.45098 0.906667
236 OVE 0.450549 0.833333
237 6AD 0.45 0.817073
238 NMN AMP PO4 0.45 0.896104
239 A5D 0.44898 0.766234
240 U A A U 0.448819 0.884615
241 MHZ 0.447917 0.701149
242 ITT 0.447917 0.842105
243 2SA 0.445545 0.883117
244 A3T 0.443299 0.824324
245 A U C C 0.442748 0.897436
246 Y3J 0.440476 0.706667
247 649 0.439655 0.728261
248 7D7 0.439024 0.746667
249 AMZ 0.438202 0.842105
250 0UM 0.438095 0.765432
251 EAD 0.4375 0.829268
252 AAT 0.435644 0.731707
253 P1H 0.435115 0.809524
254 62X 0.433962 0.709302
255 ARU 0.433962 0.795181
256 NAP 0.433071 0.92
257 71V 0.431579 0.814815
258 6C6 0.43 0.8125
259 A6D 0.429907 0.72619
260 K15 0.429907 0.72619
261 NIA 0.428571 0.780488
262 DAT 0.428571 0.810127
263 APC G U 0.427419 0.8375
264 NA0 0.426357 0.907895
265 NHD 0.42623 0.906667
266 6IA 0.425743 0.817073
267 NAD TDB 0.425676 0.663462
268 NAD NDT 0.424658 0.71134
269 SXZ 0.422018 0.73494
270 NAJ 0.421488 0.932432
271 DAL FAD PER 0.42069 0.855422
272 CNV FAD 0.41958 0.795455
273 PLP AAD 0.419355 0.744444
274 TAP 0.418605 0.860759
275 PGS 0.418367 0.814815
276 KB1 0.418182 0.743902
277 NJP 0.418033 0.896104
278 FB0 0.41791 0.786517
279 NA7 0.416667 0.858974
280 6K6 0.415094 0.905405
281 D5M 0.414894 0.807692
282 DA 0.414894 0.807692
283 0WD 0.414634 0.85
284 2VA 0.414141 0.802632
285 3NZ 0.412844 0.78481
286 ENQ 0.412844 0.917808
287 3AT 0.411765 0.868421
288 DTP 0.411765 0.810127
289 AAM 0.410526 0.891892
290 NZQ 0.409836 0.839506
291 NFD 0.408 0.884615
292 FAD NBT 0.406897 0.752688
293 8BR 0.40625 0.835443
294 GGZ 0.40566 0.761905
295 D3Y 0.40566 0.792208
296 TM1 0.405405 0.755814
297 SLU 0.404762 0.752809
298 P33 FDA 0.402685 0.788889
299 3AD 0.402299 0.808219
300 SO8 0.401961 0.792208
301 VRT 0.401961 0.772152
302 AVV 0.401869 0.82716
303 S8M 0.401869 0.719512
304 DCA 0.401575 0.804598
305 ETB 0.401575 0.813953
306 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: 63
This union binding pocket(no: 1) in the query (biounit: 4oxi.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2J5B TYE 0.02324 0.40054 2.58621
2 4OEV OXL 0.02845 0.40283 2.63158
3 3BJE R1P 0.008078 0.42445 2.86533
4 1Q11 TYE 0.02429 0.40455 2.95699
5 1FEC FAD 0.01202 0.41522 3.06122
6 1MLD CIT 0.0122 0.42002 3.18471
7 1GQ2 OXL 0.009034 0.42164 3.78378
8 4B2G V1N 0.001591 0.42611 3.81944
9 2G7C GLA GAL NAG 0.01763 0.40742 3.92157
10 5KOD AMP 0.0006868 0.46156 3.99306
11 5FPE 3TR 0.01976 0.42371 4.65116
12 5HM3 649 0.00001176 0.45524 4.6875
13 4RHS SIA SIA GAL 0.04049 0.40373 4.91803
14 3F5A SIA GAL NAG 0.0219 0.40191 5.69106
15 2BVE PH5 0.01227 0.42483 5.88235
16 1KQR MNA 0.02675 0.40423 6.14525
17 1I1E DM2 0.01648 0.41327 7.29167
18 2WZ5 MET 0.01719 0.40596 9.15033
19 3GCM 5GP 0.0151 0.43515 9.7561
20 5MST AMP 0.00000001405 0.65135 9.89583
21 5MST FUM 0.00000006016 0.5722 9.89583
22 5EY9 5SV 0.00002769 0.4683 10.0694
23 4Q3F TLA 0.02874 0.41484 10.2564
24 4K30 NLG 0.0243 0.40453 11.25
25 1MDB AMP DBH 0.0000001459 0.59971 12.8015
26 4NAE 1GP 0.02573 0.40685 13.7778
27 2Y4O DLL 0.000000008589 0.61889 14.2212
28 2Y4N PAC 0.000006524 0.52375 15.103
29 2Y4N DLL 0.0000002011 0.52113 15.103
30 2Q89 6CS 0.01751 0.40757 18.677
31 4FUT ATP 0.0000005142 0.57643 21.2724
32 4GXQ ATP 0.0000003065 0.5791 22.5296
33 1RY2 AMP 0.000000004274 0.60643 26.0417
34 1PG4 PRX 0.00000003028 0.45263 26.0417
35 1PG4 COA 0.00000003028 0.45263 26.0417
36 5OE4 3UK 0.00000001233 0.63725 26.0442
37 1V25 ANP 0.00000001241 0.51863 26.8022
38 4DG8 AMP 0.00000000009456 0.768 27.7778
39 2D1S SLU 0.00000003483 0.53577 28.1022
40 4RLQ 3SK 0.0000001678 0.46211 28.5164
41 3CW9 AMP 0.000000004425 0.68244 28.7698
42 3CW9 01A 0.0005069 0.40758 28.7698
43 5C5H 4YB 0.00000387 0.49281 29.1391
44 4R0M FA5 0.0000003379 0.52963 29.6875
45 5MSD AMP 0.0000001371 0.62456 30.9028
46 5MSD BEZ 0.00000009417 0.60779 30.9028
47 5IE3 AMP 0.000000006656 0.56966 31.9066
48 5IE3 OXD 0.000000006656 0.56966 31.9066
49 3IES M24 0.00000004612 0.50398 35.2087
50 3DHV DAL AMP 0.00000000001278 0.76164 35.7422
51 3C5E ATP 0.000000005847 0.43972 36.8421
52 3E7W AMP 0.00000000166 0.72228 38.5519
53 1AMU AMP 0.0000000001363 0.76079 39.9645
54 3O84 HTJ 0.0000067 0.49059 40.8088
55 5BSR AMP 0.00000004874 0.46732 41.3284
56 5BSR COA 0.0000001233 0.40846 41.3284
57 5X8G S0N 0.00000004231 0.4384 43.5052
58 5N9X 8QN 0.0000000001964 0.69578 43.8563
59 5N9X THR 0.000000359 0.67359 43.8563
60 5N9X ATP 0.000000002533 0.6659 43.8563
61 4D57 ARG AMP 0.00000000000008682 0.6494 44.2708
62 3NYQ AMP 0.00000001897 0.65766 45.9406
63 3NYQ MCA 0.00000002865 0.64767 45.9406
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