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 1610 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 1331 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 1144 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 (2D)
Ligand no: 1; Ligand: ARG AMP; Similar ligands found: 292
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG AMP 1 1
2 DAL AMP 0.721649 0.864198
3 GAP 0.670103 0.9
4 MYR AMP 0.611111 0.827586
5 4AD 0.609524 0.878049
6 ADP MG 0.608247 0.85
7 ADP BEF 0.608247 0.85
8 AMP MG 0.595745 0.8375
9 ANP MG 0.592233 0.819277
10 ATP MG 0.584158 0.85
11 ADP PO3 0.584158 0.85
12 BEF ADP 0.578431 0.829268
13 SRP 0.571429 0.888889
14 CA0 0.57 0.831325
15 A 0.568421 0.82716
16 AMP 0.568421 0.82716
17 5AL 0.567308 0.841463
18 A2D 0.56701 0.807229
19 KG4 0.564356 0.831325
20 YLP 0.564103 0.872093
21 VO4 ADP 0.561905 0.831325
22 ALF ADP 0.561905 0.790698
23 PTJ 0.558559 0.813953
24 8LH 0.556604 0.843373
25 AP2 0.555556 0.821429
26 BA3 0.555556 0.807229
27 A12 0.555556 0.821429
28 F2R 0.552846 0.963415
29 45A 0.55102 0.785714
30 ABM 0.55102 0.785714
31 LPA AMP 0.550847 0.827586
32 PAJ 0.550459 0.804598
33 ADP 0.55 0.829268
34 B4P 0.55 0.807229
35 YLB 0.55 0.872093
36 AP5 0.55 0.807229
37 LAD 0.54955 0.914634
38 QA7 0.546296 0.811765
39 8LQ 0.546296 0.843373
40 9ZD 0.541284 0.823529
41 8QN 0.541284 0.841463
42 9ZA 0.541284 0.823529
43 IOT 0.540984 0.951807
44 ADP BMA 0.540541 0.853659
45 AU1 0.539216 0.809524
46 APC MG 0.538462 0.829268
47 V2G 0.537736 0.879518
48 8LE 0.537736 0.811765
49 YLC 0.53719 0.892857
50 AMO 0.536364 0.865854
51 50T 0.533981 0.797619
52 ATP 0.533981 0.829268
53 HEJ 0.533981 0.829268
54 AYB 0.532258 0.862069
55 AHX 0.531532 0.835294
56 NB8 0.530973 0.835294
57 TXA 0.530973 0.821429
58 ME8 0.530973 0.827586
59 SRA 0.530612 0.788235
60 GJV 0.53 0.875
61 AT4 0.529412 0.8
62 AN2 0.529412 0.819277
63 ALF ADP 3PG 0.528926 0.825581
64 AR6 0.528846 0.829268
65 5FA 0.528846 0.829268
66 PRX 0.528846 0.788235
67 APR 0.528846 0.829268
68 AQP 0.528846 0.829268
69 APC 0.528846 0.821429
70 ADX 0.524272 0.736264
71 M33 0.524272 0.797619
72 YLA 0.524194 0.872093
73 RBY 0.52381 0.821429
74 AGS 0.52381 0.790698
75 AD9 0.52381 0.809524
76 ADV 0.52381 0.821429
77 WAQ 0.522124 0.86747
78 9SN 0.521739 0.793103
79 AMP DBH 0.521368 0.809524
80 ACP 0.519231 0.831325
81 DLL 0.517857 0.841463
82 1ZZ 0.517544 0.806818
83 AHZ 0.516667 0.806818
84 AF3 ADP 3PG 0.516393 0.825581
85 6RE 0.515152 0.8625
86 SON 0.514563 0.865854
87 ANP 0.514019 0.809524
88 OOB 0.513514 0.841463
89 5SV 0.513514 0.772727
90 XAH 0.512821 0.870588
91 AR6 AR6 0.512605 0.851852
92 AMP NAD 0.511811 0.864198
93 HQG 0.509091 0.841463
94 A1R 0.508929 0.845238
95 NSS 0.508929 0.752688
96 B5V 0.508772 0.821429
97 ATF 0.504587 0.8
98 A22 0.504505 0.819277
99 00A 0.504425 0.802326
100 NVA LMS 0.504425 0.747368
101 FA5 0.504274 0.865854
102 ATP A 0.504274 0.839506
103 ATP A A A 0.504274 0.839506
104 N0B 0.503759 0.872093
105 T99 0.5 0.8
106 LEU LMS 0.5 0.763441
107 3UK 0.5 0.831325
108 ACQ 0.5 0.831325
109 9X8 0.5 0.790698
110 OAD 0.5 0.831325
111 7MD 0.5 0.892857
112 TAT 0.5 0.8
113 NAD IBO 0.5 0.851852
114 NAD TDB 0.5 0.851852
115 PR8 0.495652 0.903614
116 ADQ 0.495575 0.831325
117 YLY 0.492424 0.862069
118 BIS 0.491379 0.823529
119 3OD 0.491379 0.831325
120 JNT 0.491228 0.831325
121 MAP 0.491071 0.790698
122 G5A 0.490741 0.771739
123 5AS 0.490385 0.715789
124 LMS 0.49 0.717391
125 NAJ PZO 0.48855 0.793103
126 25A 0.486726 0.829268
127 6YZ 0.486486 0.831325
128 SSA 0.486486 0.752688
129 NAI 0.483871 0.781609
130 TAD 0.483607 0.784091
131 A3R 0.482456 0.845238
132 OMR 0.48 0.797753
133 B5M 0.478992 0.811765
134 B5Y 0.478992 0.811765
135 FYA 0.478632 0.819277
136 TSB 0.477876 0.712766
137 53H 0.477876 0.697917
138 A5A 0.477477 0.72043
139 COD 0.476923 0.822222
140 NAD 0.476923 0.841463
141 AP0 0.47619 0.752809
142 48N 0.475806 0.857143
143 25L 0.474576 0.819277
144 NAJ PYZ 0.474074 0.758242
145 NAQ 0.474074 0.793103
146 OZV 0.473684 0.807229
147 DQV 0.471545 0.819277
148 4UV 0.471074 0.811765
149 KAA 0.470085 0.784946
150 A3D 0.469697 0.831325
151 LSS 0.469565 0.71875
152 54H 0.469027 0.705263
153 52H 0.469027 0.697917
154 VMS 0.469027 0.705263
155 TYM 0.468254 0.865854
156 TXE 0.468254 0.802326
157 LAQ 0.467742 0.806818
158 NAE 0.466667 0.811765
159 JB6 0.466102 0.802326
160 AOC 0.466019 0.722892
161 5CA 0.464912 0.752688
162 7MC 0.464567 0.872093
163 4UU 0.463415 0.811765
164 AFH 0.463415 0.804598
165 J7C 0.461538 0.85
166 GEK 0.46087 0.77381
167 6V0 0.460317 0.793103
168 TXD 0.460317 0.802326
169 DND 0.460317 0.843373
170 ZID 0.459854 0.831325
171 80F 0.458647 0.788889
172 5CD 0.458333 0.707317
173 GSU 0.457627 0.771739
174 P5A 0.457627 0.776596
175 RAB 0.457447 0.740741
176 XYA 0.457447 0.740741
177 ADN 0.457447 0.740741
178 0UM 0.456897 0.776471
179 DSZ 0.456897 0.752688
180 3DH 0.455446 0.682353
181 G3A 0.455285 0.857143
182 KMQ 0.454545 0.8
183 L3W 0.453125 0.8
184 8X1 0.452174 0.765957
185 G5P 0.451613 0.857143
186 KYE 0.45082 0.855422
187 SFG 0.449541 0.765432
188 5X8 0.449541 0.756098
189 H1Q 0.449541 0.795181
190 NAX 0.448819 0.816092
191 4UW 0.448819 0.784091
192 5N5 0.447917 0.740741
193 S7M 0.447368 0.727273
194 J4G 0.445378 0.901235
195 NDC 0.444444 0.835294
196 A3S 0.444444 0.777778
197 4TA 0.443609 0.797753
198 A4D 0.443299 0.719512
199 THR ARG SER GLY FZN VAL MET ARG ARG LEU 0.443182 0.831579
200 EEM 0.442478 0.727273
201 9K8 0.441667 0.676768
202 SA8 0.441441 0.744186
203 NDE 0.440559 0.843373
204 BT5 0.440298 0.840909
205 GA7 0.44 0.8
206 DTA 0.44 0.694118
207 CNA 0.439394 0.843373
208 YSA 0.439024 0.734043
209 A4P 0.438462 0.852273
210 NEC 0.438095 0.698795
211 SAI 0.4375 0.75
212 UP5 0.4375 0.790698
213 SAH 0.4375 0.759036
214 K15 0.436975 0.738636
215 PO4 PO4 A A A A PO4 0.436975 0.814815
216 GTA 0.436508 0.848837
217 Z5A 0.435714 0.771739
218 SMM 0.434783 0.722222
219 SAM 0.433628 0.727273
220 6IA 0.433628 0.825581
221 NMN AMP PO4 0.432836 0.811765
222 ADJ 0.431818 0.797753
223 139 0.431818 0.795455
224 7D5 0.431373 0.77381
225 8PZ 0.430894 0.734043
226 EP4 0.43 0.686047
227 DZD 0.42963 0.804598
228 M24 0.427536 0.775281
229 B1U 0.427419 0.69697
230 KY2 0.42735 0.831325
231 FME ARG THR GLY ASN ALA ASP ND7 0.426035 0.879121
232 A3P 0.425926 0.82716
233 A2P 0.425926 0.814815
234 M2T 0.425743 0.670455
235 A3G 0.424528 0.790123
236 DSH 0.424528 0.761905
237 EAD 0.422535 0.775281
238 BTX 0.422222 0.829545
239 MTA 0.421569 0.682353
240 COA FLC 0.421429 0.842697
241 V3L 0.421053 0.851852
242 T5A 0.421053 0.769231
243 P1H 0.42069 0.777778
244 A3N 0.420561 0.714286
245 KYB 0.420168 0.831325
246 4TC 0.419847 0.793103
247 UPA 0.419847 0.802326
248 ZAS 0.419048 0.759036
249 62X 0.416667 0.722222
250 6MZ 0.416667 0.795181
251 S4M 0.416667 0.722222
252 7D3 0.416667 0.776471
253 ATR 0.415929 0.804878
254 NVA 2AD 0.415929 0.77381
255 PAP 0.415929 0.817073
256 FB0 0.414966 0.815217
257 NDP DTT 0.414966 0.788889
258 7D4 0.414414 0.776471
259 MHZ 0.414414 0.714286
260 D4F 0.414286 0.827586
261 NWW 0.414141 0.666667
262 KXW 0.414062 0.785714
263 KH3 0.414062 0.75
264 2SA 0.413793 0.865854
265 QXG 0.413223 0.712766
266 N01 0.413043 0.841463
267 O02 0.412281 0.813953
268 WSA 0.412214 0.741935
269 QXP 0.411765 0.72043
270 N5O 0.411215 0.777778
271 A3T 0.410714 0.743902
272 3AM 0.409524 0.814815
273 7C5 0.409449 0.829268
274 2A5 0.40708 0.831325
275 A2R 0.40678 0.841463
276 SXZ 0.406504 0.727273
277 A7D 0.405405 0.746988
278 6NA COA 0.405229 0.806452
279 NAD BBN 0.405229 0.788889
280 HY8 0.40458 0.788235
281 N5A 0.40367 0.753086
282 4YB 0.403101 0.755319
283 OVE 0.401869 0.776471
284 649 0.401515 0.739583
285 2AM 0.4 0.804878
286 VRT 0.4 0.761905
287 HZ2 0.4 0.788235
288 MAO 0.4 0.733333
289 DCA 0.4 0.813187
290 NAD CJ3 0.4 0.763441
291 BUA COA 0.4 0.824176
292 FAM 0.4 0.815217
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG AMP; Similar ligands found: 1
No: Ligand Similarity coefficient
1 TYR AMP 0.9540
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
APoc FAQ
Feedback