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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 1443 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 1205 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 1039 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: 259
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 PO3 0.584158 0.85
8 SRP 0.571429 0.888889
9 ADP VO4 0.571429 0.819277
10 VO4 ADP 0.571429 0.819277
11 CA0 0.57 0.831325
12 A 0.568421 0.82716
13 AMP 0.568421 0.82716
14 5AL 0.567308 0.841463
15 A2D 0.56701 0.807229
16 YLP 0.564103 0.872093
17 ADP ALF 0.561905 0.790698
18 ALF ADP 0.561905 0.790698
19 PTJ 0.558559 0.813953
20 BA3 0.555556 0.807229
21 A12 0.555556 0.821429
22 AP2 0.555556 0.821429
23 F2R 0.552846 0.963415
24 ABM 0.55102 0.785714
25 LPA AMP 0.550847 0.827586
26 PAJ 0.550459 0.804598
27 AP5 0.55 0.807229
28 YLB 0.55 0.872093
29 ADP 0.55 0.829268
30 B4P 0.55 0.807229
31 LAD 0.54955 0.914634
32 9ZA 0.541284 0.823529
33 8QN 0.541284 0.841463
34 9ZD 0.541284 0.823529
35 IOT 0.540984 0.951807
36 ADP BMA 0.540541 0.853659
37 AU1 0.539216 0.809524
38 YLC 0.53719 0.892857
39 AMO 0.536364 0.865854
40 50T 0.533981 0.797619
41 HEJ 0.533981 0.829268
42 ATP 0.533981 0.829268
43 AYB 0.532258 0.862069
44 AHX 0.531532 0.835294
45 TXA 0.530973 0.821429
46 ME8 0.530973 0.827586
47 NB8 0.530973 0.835294
48 SRA 0.530612 0.788235
49 GJV 0.53 0.875
50 AN2 0.529412 0.819277
51 AT4 0.529412 0.8
52 5FA 0.528846 0.829268
53 APR 0.528846 0.829268
54 APC 0.528846 0.821429
55 AR6 0.528846 0.829268
56 AQP 0.528846 0.829268
57 PRX 0.528846 0.788235
58 M33 0.524272 0.797619
59 ADX 0.524272 0.736264
60 YLA 0.524194 0.872093
61 RBY 0.52381 0.821429
62 ADV 0.52381 0.821429
63 AD9 0.52381 0.809524
64 AGS 0.52381 0.790698
65 SAP 0.52381 0.790698
66 A A 0.522124 0.829268
67 WAQ 0.522124 0.86747
68 9SN 0.521739 0.793103
69 AMP DBH 0.521368 0.809524
70 ACP 0.519231 0.831325
71 DLL 0.517857 0.841463
72 1ZZ 0.517544 0.806818
73 AHZ 0.516667 0.806818
74 AF3 ADP 3PG 0.516393 0.825581
75 6RE 0.515152 0.8625
76 SON 0.514563 0.865854
77 ANP 0.514019 0.809524
78 5SV 0.513514 0.772727
79 OOB 0.513514 0.841463
80 XAH 0.512821 0.870588
81 AR6 AR6 0.512605 0.851852
82 AMP NAD 0.511811 0.864198
83 NSS 0.508929 0.752688
84 A1R 0.508929 0.845238
85 B5V 0.508772 0.821429
86 ATF 0.504587 0.8
87 A22 0.504505 0.819277
88 NVA LMS 0.504425 0.747368
89 00A 0.504425 0.802326
90 YAP 0.504274 0.855422
91 FA5 0.504274 0.865854
92 ATP A A A 0.504274 0.839506
93 N0B 0.503759 0.872093
94 7MD 0.5 0.892857
95 3UK 0.5 0.831325
96 OAD 0.5 0.831325
97 ACQ 0.5 0.831325
98 TAT 0.5 0.8
99 9X8 0.5 0.790698
100 T99 0.5 0.8
101 PR8 0.495652 0.903614
102 ADQ 0.495575 0.831325
103 YLY 0.492424 0.862069
104 3OD 0.491379 0.831325
105 BIS 0.491379 0.823529
106 MAP 0.491071 0.790698
107 G5A 0.490741 0.771739
108 5AS 0.490385 0.715789
109 LMS 0.49 0.717391
110 NAJ PZO 0.48855 0.793103
111 LEU LMS 0.486957 0.729167
112 25A 0.486726 0.829268
113 SSA 0.486486 0.752688
114 6YZ 0.486486 0.831325
115 NAI 0.483871 0.781609
116 TAD 0.483607 0.784091
117 A3R 0.482456 0.845238
118 OMR 0.48 0.797753
119 B5Y 0.478992 0.811765
120 B5M 0.478992 0.811765
121 FYA 0.478632 0.819277
122 53H 0.477876 0.697917
123 TSB 0.477876 0.712766
124 A5A 0.477477 0.72043
125 COD 0.476923 0.822222
126 NAD 0.476923 0.841463
127 AP0 0.47619 0.752809
128 48N 0.475806 0.857143
129 25L 0.474576 0.819277
130 NAQ 0.474074 0.793103
131 NAJ PYZ 0.474074 0.758242
132 DQV 0.471545 0.819277
133 4UV 0.471074 0.811765
134 KAA 0.470085 0.784946
135 A3D 0.469697 0.831325
136 LSS 0.469565 0.71875
137 54H 0.469027 0.705263
138 VMS 0.469027 0.705263
139 52H 0.469027 0.697917
140 TYM 0.468254 0.865854
141 TXE 0.468254 0.802326
142 LAQ 0.467742 0.806818
143 NAE 0.466667 0.811765
144 JB6 0.466102 0.802326
145 AOC 0.466019 0.722892
146 5CA 0.464912 0.752688
147 7MC 0.464567 0.872093
148 4UU 0.463415 0.811765
149 AFH 0.463415 0.804598
150 J7C 0.461538 0.85
151 GEK 0.46087 0.77381
152 TXD 0.460317 0.802326
153 NXX 0.460317 0.843373
154 DND 0.460317 0.843373
155 6V0 0.460317 0.793103
156 ZID 0.459854 0.831325
157 80F 0.458647 0.788889
158 5CD 0.458333 0.707317
159 P5A 0.457627 0.776596
160 GSU 0.457627 0.771739
161 ADN 0.457447 0.740741
162 RAB 0.457447 0.740741
163 XYA 0.457447 0.740741
164 DSZ 0.456897 0.752688
165 0UM 0.456897 0.776471
166 3DH 0.455446 0.682353
167 G3A 0.455285 0.857143
168 U A 0.455224 0.823529
169 8X1 0.452174 0.765957
170 G5P 0.451613 0.857143
171 SFG 0.449541 0.765432
172 5X8 0.449541 0.756098
173 NAX 0.448819 0.816092
174 4UW 0.448819 0.784091
175 5N5 0.447917 0.740741
176 S7M 0.447368 0.727273
177 THR ARG SER GLY FZN VAL MET ARG ARG LEU 0.446328 0.831579
178 NDC 0.444444 0.835294
179 A3S 0.444444 0.777778
180 4TA 0.443609 0.797753
181 G A A A 0.443609 0.902439
182 A G 0.443609 0.890244
183 A4D 0.443299 0.719512
184 EEM 0.442478 0.727273
185 9K8 0.441667 0.676768
186 SA8 0.441441 0.744186
187 NDE 0.440559 0.843373
188 U A G G 0.440298 0.890244
189 BT5 0.440298 0.840909
190 GA7 0.44 0.8
191 DTA 0.44 0.694118
192 CNA 0.439394 0.843373
193 YSA 0.439024 0.734043
194 A4P 0.438462 0.852273
195 NEC 0.438095 0.698795
196 SAI 0.4375 0.75
197 SAH 0.4375 0.759036
198 UP5 0.4375 0.790698
199 K15 0.436975 0.738636
200 PO4 PO4 A A A A PO4 0.436975 0.814815
201 GTA 0.436508 0.848837
202 Z5A 0.435714 0.771739
203 SMM 0.434783 0.722222
204 SAM 0.433628 0.727273
205 6IA 0.433628 0.825581
206 NMN AMP PO4 0.432836 0.811765
207 139 0.431818 0.795455
208 ADJ 0.431818 0.797753
209 7D5 0.431373 0.77381
210 8PZ 0.430894 0.734043
211 EP4 0.43 0.686047
212 DZD 0.42963 0.804598
213 M24 0.427536 0.775281
214 A3P 0.425926 0.82716
215 A2P 0.425926 0.814815
216 M2T 0.425743 0.670455
217 A A A 0.425 0.841463
218 A3G 0.424528 0.790123
219 DSH 0.424528 0.761905
220 EAD 0.422535 0.775281
221 BTX 0.422222 0.829545
222 MTA 0.421569 0.682353
223 V3L 0.421053 0.851852
224 T5A 0.421053 0.769231
225 P1H 0.42069 0.777778
226 A3N 0.420561 0.714286
227 UPA 0.419847 0.802326
228 4TC 0.419847 0.793103
229 ZAS 0.419048 0.759036
230 A U 0.416667 0.833333
231 62X 0.416667 0.722222
232 S4M 0.416667 0.722222
233 7D3 0.416667 0.776471
234 NVA 2AD 0.415929 0.77381
235 ATR 0.415929 0.804878
236 PAP 0.415929 0.817073
237 FB0 0.414966 0.815217
238 MHZ 0.414414 0.714286
239 7D4 0.414414 0.776471
240 KH3 0.414062 0.75
241 2SA 0.413793 0.865854
242 N01 0.413043 0.841463
243 WSA 0.412214 0.741935
244 A3T 0.410714 0.743902
245 3AM 0.409524 0.814815
246 7C5 0.409449 0.829268
247 2A5 0.40708 0.831325
248 A2R 0.40678 0.841463
249 SXZ 0.406504 0.727273
250 A7D 0.405405 0.746988
251 4YB 0.403101 0.755319
252 A C A C 0.402878 0.857143
253 OVE 0.401869 0.776471
254 649 0.401515 0.739583
255 DCA 0.4 0.813187
256 VRT 0.4 0.761905
257 MAO 0.4 0.733333
258 2AM 0.4 0.804878
259 FAM 0.4 0.815217
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: 145
This union binding pocket(no: 1) in the query (biounit: 4d57.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 5CQG 55C 1.22164
3 3EXS 5RP 1.35747
4 2G7C GLA GAL NAG 1.96078
5 1Q19 SSC 1.98807
6 1H5R THM 2.04778
7 2GJP MAL 2.06186
8 1H3F TYE 2.08333
9 3B2Q AES 2.1322
10 3LTW HLZ 2.14286
11 2AAZ CB3 2.2082
12 3TAO PGH 2.24719
13 1BW9 PPY 2.24719
14 1BXG HCI 2.24719
15 1C1X HFA 2.25352
16 2A9W GA9 2.27273
17 5C9P FUC 2.3622
18 1H74 ILE 2.36486
19 1L7P SEP 2.36967
20 1L7N ALF 2.36967
21 4B2D SER 2.37226
22 1V6A TRE 2.40964
23 5O2N FLC 2.44328
24 3KCC CMP 2.44328
25 5VKM GAL SIA 2.46914
26 2Y4O DLL 2.48307
27 5WXU FLC 2.50522
28 2ZUX RAM 2.53807
29 1D8T GDP 2.54453
30 1C3X 8IG 2.63158
31 1J1R ADE 2.68199
32 6E1Q CFA 2.79232
33 3GVL SLB SIA 2.79232
34 3QPB R1P 2.83688
35 1W8S FBP 3.04183
36 5LX6 78P 3.14136
37 5H4S RAM 3.16901
38 3A06 NDP 3.19149
39 3ZZH NLG 3.25733
40 3ZZH ARG 3.25733
41 5W5R PYR 3.34928
42 5FPE 3TR 3.35917
43 3UEC ALA ARG TPO LYS 3.42466
44 5KOD AMP 3.4904
45 4PTN GXV 3.4904
46 3BJE R1P 3.72493
47 5XNC MTA 3.77358
48 3JQQ A2P 3.79747
49 2BQP GLC 3.84615
50 4KBA 1QM 3.92749
51 4BG4 ARG 3.93258
52 1X8X TYR 4.03727
53 2YPI PGA 4.04858
54 1S8G DAO 4.13223
55 1Q6O LG6 4.16667
56 5M6N 7H9 4.23729
57 4OEV OXL 4.25101
58 4URX HXY 4.31212
59 5BN3 ADP 4.363
60 1GPM AMP 4.38095
61 5DEQ ARA 4.38596
62 1E5F PLP 4.45545
63 5MB4 NAG 4.48878
64 5IGL BMF 4.51613
65 3A6T 8OG 4.65116
66 1FDJ 13P 4.6832
67 1QDS PGA 4.78088
68 4V3C C 4.89691
69 2IV3 UDP 4.97076
70 4TS1 TYR 5.01567
71 2F6U CIT 5.12821
72 1BC5 ACE ASN TRP GLU THR PHE 5.20446
73 2WPW ACO 5.60472
74 3FSY SCA 5.72289
75 1LYX PGA 5.75916
76 4EPM AMP 5.85198
77 1C3M MAN MAN 6.12245
78 2PKA BEN 6.25
79 1QD0 RR6 6.25
80 1VKF CIT 6.38298
81 5XQW 8EU 6.45161
82 3ZGJ RMN 6.469
83 6BSW UDP 6.50888
84 6G5J EM8 6.66667
85 2X1L ADN 6.87023
86 3W6X HZP 6.9869
87 1L5Y BEF 7.09677
88 4OVZ P85 7.27848
89 4OFJ HIS 7.39958
90 4Z87 GDP 7.80952
91 5TCI MLI 7.97101
92 3MYZ TFX 8
93 1QAW TRP 8.10811
94 3P2H NOO 8.45771
95 3KIF GDL 8.49057
96 1HSL HIS 8.82353
97 2BVE PH5 9.2437
98 1I1E DM2 9.77312
99 3T64 DU3 9.94475
100 2WG9 OCA 10.7692
101 4NAE 1GP 11.1111
102 2VQZ MGT 12.0482
103 1YZG GDP 12.2905
104 3H0L ADP 17.0213
105 3HCH RSM 17.1233
106 1SW0 PGA 18.1452
107 4JEJ 1GP 22.9508
108 3CT5 NAG NAG NAG 23.2704
109 5MST AMP 25.4799
110 5MST FUM 25.4799
111 5MSD BEZ 28.0977
112 5MSD AMP 28.0977
113 5HM3 649 28.4468
114 5EY9 5SV 28.9703
115 3KXW 1ZZ 32.1117
116 5D6J ATP 32.2862
117 1LES GLC FRU 32.6923
118 5OE4 3UK 36.3636
119 1PG4 PRX 37.1728
120 1PG4 COA 37.1728
121 1RY2 AMP 37.3473
122 3IES M24 38.657
123 1MDB AMP DBH 39.5176
124 2D1S SLU 39.5985
125 3C5E ATP 40.1754
126 4FUT ATP 40.7555
127 5WM2 SAL 41.1348
128 5WM2 AMP 41.1348
129 1V25 ANP 41.22
130 5BSR COA 41.6974
131 5BSR AMP 41.6974
132 4GXQ ATP 41.6996
133 4RLQ 3SK 42.0039
134 4DG8 AMP 42.0593
135 3O84 HTJ 42.4632
136 5X8G S0N 43.0928
137 2V7B BEZ 43.4783
138 3NYQ AMP 43.5644
139 3NYQ MCA 43.5644
140 3CW9 AMP 43.8492
141 3CW9 01A 43.8492
142 4OXI GAP 44.2708
143 5IE3 OXD 44.358
144 5IE3 AMP 44.358
145 5C5H 4YB 45.4746
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