Receptor
PDB id Resolution Class Description Source Keywords
4D57 2 Å NON-ENZYME: OTHER UNDERSTANDING BI-SPECIFICITY OF A-DOMAINS PLANKTOTHRIX AGARDHII TRANSCRIPTION NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATIONDOMAIN
Ref.: STRUCTURAL ELUCIDATION OF THE BISPECIFICITY OF A DO A BASIS FOR ACTIVATING NON-NATURAL AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 8833 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG AMP A:1491;
Valid;
none;
submit data
504.421 n/a P(=O)...
GOL A:1492;
A:1493;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PO4 A:1494;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D57 2 Å NON-ENZYME: OTHER UNDERSTANDING BI-SPECIFICITY OF A-DOMAINS PLANKTOTHRIX AGARDHII TRANSCRIPTION NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATIONDOMAIN
Ref.: STRUCTURAL ELUCIDATION OF THE BISPECIFICITY OF A DO A BASIS FOR ACTIVATING NON-NATURAL AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 8833 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1130 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
5 1AMU - AMP C10 H14 N5 O7 P c1nc(c2c(n....
6 5N81 - 8Q2 C22 H25 N7 O8 S C#CCOc1ccc....
7 5N82 - 8PZ C19 H23 N7 O7 S c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG AMP; Similar ligands found: 279
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG AMP 1 1
2 DAL AMP 0.721649 0.864198
3 TYR AMP 0.695238 0.878049
4 GAP 0.670103 0.9
5 MYR AMP 0.611111 0.827586
6 4AD 0.609524 0.878049
7 ADP MG 0.608247 0.85
8 ATP MG 0.584158 0.85
9 ADP PO3 0.584158 0.85
10 SRP 0.571429 0.888889
11 ADP VO4 0.571429 0.819277
12 VO4 ADP 0.571429 0.819277
13 CA0 0.57 0.831325
14 A 0.568421 0.82716
15 AMP 0.568421 0.82716
16 5AL 0.567308 0.841463
17 A2D 0.56701 0.807229
18 KG4 0.564356 0.831325
19 YLP 0.564103 0.872093
20 ADP ALF 0.561905 0.790698
21 ALF ADP 0.561905 0.790698
22 PTJ 0.558559 0.813953
23 8LH 0.556604 0.843373
24 AP2 0.555556 0.821429
25 A12 0.555556 0.821429
26 BA3 0.555556 0.807229
27 F2R 0.552846 0.963415
28 ABM 0.55102 0.785714
29 45A 0.55102 0.785714
30 LPA AMP 0.550847 0.827586
31 PAJ 0.550459 0.804598
32 YLB 0.55 0.872093
33 B4P 0.55 0.807229
34 ADP 0.55 0.829268
35 AP5 0.55 0.807229
36 LAD 0.54955 0.914634
37 8LQ 0.546296 0.843373
38 9ZD 0.541284 0.823529
39 8QN 0.541284 0.841463
40 9ZA 0.541284 0.823529
41 IOT 0.540984 0.951807
42 ADP BMA 0.540541 0.853659
43 AU1 0.539216 0.809524
44 APC MG 0.538462 0.829268
45 8LE 0.537736 0.811765
46 YLC 0.53719 0.892857
47 AMO 0.536364 0.865854
48 50T 0.533981 0.797619
49 ATP 0.533981 0.829268
50 HEJ 0.533981 0.829268
51 AYB 0.532258 0.862069
52 AHX 0.531532 0.835294
53 ME8 0.530973 0.827586
54 NB8 0.530973 0.835294
55 TXA 0.530973 0.821429
56 SRA 0.530612 0.788235
57 GJV 0.53 0.875
58 AT4 0.529412 0.8
59 AN2 0.529412 0.819277
60 APR 0.528846 0.829268
61 5FA 0.528846 0.829268
62 AQP 0.528846 0.829268
63 PRX 0.528846 0.788235
64 APC 0.528846 0.821429
65 AR6 0.528846 0.829268
66 M33 0.524272 0.797619
67 ADX 0.524272 0.736264
68 YLA 0.524194 0.872093
69 RBY 0.52381 0.821429
70 ADV 0.52381 0.821429
71 SAP 0.52381 0.790698
72 AD9 0.52381 0.809524
73 AGS 0.52381 0.790698
74 A A 0.522124 0.829268
75 WAQ 0.522124 0.86747
76 9SN 0.521739 0.793103
77 AMP DBH 0.521368 0.809524
78 ACP 0.519231 0.831325
79 DLL 0.517857 0.841463
80 1ZZ 0.517544 0.806818
81 AHZ 0.516667 0.806818
82 AF3 ADP 3PG 0.516393 0.825581
83 6RE 0.515152 0.8625
84 SON 0.514563 0.865854
85 ANP 0.514019 0.809524
86 5SV 0.513514 0.772727
87 OOB 0.513514 0.841463
88 XAH 0.512821 0.870588
89 AR6 AR6 0.512605 0.851852
90 AMP NAD 0.511811 0.864198
91 HQG 0.509091 0.841463
92 NSS 0.508929 0.752688
93 A1R 0.508929 0.845238
94 B5V 0.508772 0.821429
95 ATF 0.504587 0.8
96 A22 0.504505 0.819277
97 00A 0.504425 0.802326
98 NVA LMS 0.504425 0.747368
99 ATP A 0.504274 0.839506
100 YAP 0.504274 0.855422
101 ATP A A A 0.504274 0.839506
102 FA5 0.504274 0.865854
103 N0B 0.503759 0.872093
104 9X8 0.5 0.790698
105 3UK 0.5 0.831325
106 OAD 0.5 0.831325
107 7MD 0.5 0.892857
108 TAT 0.5 0.8
109 ACQ 0.5 0.831325
110 T99 0.5 0.8
111 PR8 0.495652 0.903614
112 ADQ 0.495575 0.831325
113 YLY 0.492424 0.862069
114 3OD 0.491379 0.831325
115 BIS 0.491379 0.823529
116 MAP 0.491071 0.790698
117 G5A 0.490741 0.771739
118 5AS 0.490385 0.715789
119 LMS 0.49 0.717391
120 NAJ PZO 0.48855 0.793103
121 LEU LMS 0.486957 0.729167
122 25A 0.486726 0.829268
123 SSA 0.486486 0.752688
124 6YZ 0.486486 0.831325
125 NAI 0.483871 0.781609
126 TAD 0.483607 0.784091
127 A3R 0.482456 0.845238
128 OMR 0.48 0.797753
129 B5M 0.478992 0.811765
130 B5Y 0.478992 0.811765
131 FYA 0.478632 0.819277
132 TSB 0.477876 0.712766
133 53H 0.477876 0.697917
134 A5A 0.477477 0.72043
135 NAD 0.476923 0.841463
136 COD 0.476923 0.822222
137 AP0 0.47619 0.752809
138 48N 0.475806 0.857143
139 25L 0.474576 0.819277
140 NAQ 0.474074 0.793103
141 NAJ PYZ 0.474074 0.758242
142 OZV 0.473684 0.807229
143 DQV 0.471545 0.819277
144 4UV 0.471074 0.811765
145 KAA 0.470085 0.784946
146 A3D 0.469697 0.831325
147 LSS 0.469565 0.71875
148 VMS 0.469027 0.705263
149 52H 0.469027 0.697917
150 54H 0.469027 0.705263
151 TYM 0.468254 0.865854
152 TXE 0.468254 0.802326
153 LAQ 0.467742 0.806818
154 NAE 0.466667 0.811765
155 JB6 0.466102 0.802326
156 AOC 0.466019 0.722892
157 5CA 0.464912 0.752688
158 7MC 0.464567 0.872093
159 AFH 0.463415 0.804598
160 4UU 0.463415 0.811765
161 J7C 0.461538 0.85
162 GEK 0.46087 0.77381
163 TXD 0.460317 0.802326
164 DND 0.460317 0.843373
165 NXX 0.460317 0.843373
166 6V0 0.460317 0.793103
167 ZID 0.459854 0.831325
168 80F 0.458647 0.788889
169 5CD 0.458333 0.707317
170 GSU 0.457627 0.771739
171 P5A 0.457627 0.776596
172 ADN 0.457447 0.740741
173 RAB 0.457447 0.740741
174 XYA 0.457447 0.740741
175 DSZ 0.456897 0.752688
176 0UM 0.456897 0.776471
177 3DH 0.455446 0.682353
178 G3A 0.455285 0.857143
179 U A 0.455224 0.823529
180 8X1 0.452174 0.765957
181 G5P 0.451613 0.857143
182 SFG 0.449541 0.765432
183 H1Q 0.449541 0.795181
184 5X8 0.449541 0.756098
185 NAX 0.448819 0.816092
186 4UW 0.448819 0.784091
187 5N5 0.447917 0.740741
188 S7M 0.447368 0.727273
189 THR ARG SER GLY FZN VAL MET ARG ARG LEU 0.446328 0.831579
190 J4G 0.445378 0.901235
191 A3S 0.444444 0.777778
192 NDC 0.444444 0.835294
193 A G 0.443609 0.890244
194 G A A A 0.443609 0.902439
195 4TA 0.443609 0.797753
196 A4D 0.443299 0.719512
197 EEM 0.442478 0.727273
198 9K8 0.441667 0.676768
199 SA8 0.441441 0.744186
200 NDE 0.440559 0.843373
201 U A G G 0.440298 0.890244
202 BT5 0.440298 0.840909
203 DTA 0.44 0.694118
204 GA7 0.44 0.8
205 CNA 0.439394 0.843373
206 YSA 0.439024 0.734043
207 A4P 0.438462 0.852273
208 NEC 0.438095 0.698795
209 SAH 0.4375 0.759036
210 SAI 0.4375 0.75
211 UP5 0.4375 0.790698
212 PO4 PO4 A A A A PO4 0.436975 0.814815
213 K15 0.436975 0.738636
214 GTA 0.436508 0.848837
215 Z5A 0.435714 0.771739
216 SMM 0.434783 0.722222
217 SAM 0.433628 0.727273
218 6IA 0.433628 0.825581
219 NMN AMP PO4 0.432836 0.811765
220 ADJ 0.431818 0.797753
221 139 0.431818 0.795455
222 7D5 0.431373 0.77381
223 8PZ 0.430894 0.734043
224 EP4 0.43 0.686047
225 DZD 0.42963 0.804598
226 M24 0.427536 0.775281
227 B1U 0.427419 0.69697
228 A3P 0.425926 0.82716
229 A2P 0.425926 0.814815
230 M2T 0.425743 0.670455
231 A A A 0.425 0.841463
232 A3G 0.424528 0.790123
233 DSH 0.424528 0.761905
234 EAD 0.422535 0.775281
235 BTX 0.422222 0.829545
236 MTA 0.421569 0.682353
237 COA FLC 0.421429 0.842697
238 T5A 0.421053 0.769231
239 V3L 0.421053 0.851852
240 P1H 0.42069 0.777778
241 A3N 0.420561 0.714286
242 4TC 0.419847 0.793103
243 UPA 0.419847 0.802326
244 ZAS 0.419048 0.759036
245 7D3 0.416667 0.776471
246 6MZ 0.416667 0.795181
247 62X 0.416667 0.722222
248 S4M 0.416667 0.722222
249 A U 0.416667 0.833333
250 NVA 2AD 0.415929 0.77381
251 PAP 0.415929 0.817073
252 ATR 0.415929 0.804878
253 FB0 0.414966 0.815217
254 MHZ 0.414414 0.714286
255 7D4 0.414414 0.776471
256 KH3 0.414062 0.75
257 2SA 0.413793 0.865854
258 N01 0.413043 0.841463
259 WSA 0.412214 0.741935
260 N5O 0.411215 0.777778
261 A3T 0.410714 0.743902
262 3AM 0.409524 0.814815
263 7C5 0.409449 0.829268
264 2A5 0.40708 0.831325
265 A2R 0.40678 0.841463
266 SXZ 0.406504 0.727273
267 A7D 0.405405 0.746988
268 HY8 0.40458 0.788235
269 N5A 0.40367 0.753086
270 4YB 0.403101 0.755319
271 A C A C 0.402878 0.857143
272 OVE 0.401869 0.776471
273 649 0.401515 0.739583
274 VRT 0.4 0.761905
275 MAO 0.4 0.733333
276 DCA 0.4 0.813187
277 HZ2 0.4 0.788235
278 FAM 0.4 0.815217
279 2AM 0.4 0.804878
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D57; Ligand: ARG AMP; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4d57.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 6IJB AMP 38.7755
2 6IJB A8C 38.7755
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