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+](...
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 1256 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 1068 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 (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 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....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG AMP; Similar ligands found: 230
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG AMP 1 1
2 DAL AMP 0.707071 0.864198
3 TYR AMP 0.688679 0.865854
4 GAP 0.64 0.9
5 ADP MG 0.59 0.819277
6 MYR AMP 0.585586 0.827586
7 BEF ADP 0.584158 0.8
8 ADP BEF 0.584158 0.8
9 AMP MG 0.57732 0.807229
10 ADP PO3 0.572816 0.85
11 LPA AMP 0.567797 0.827586
12 ATP MG 0.567308 0.819277
13 ALF ADP 0.566038 0.790698
14 ADP ALF 0.566038 0.790698
15 ANP MG 0.560748 0.790698
16 CA0 0.558824 0.831325
17 AF3 ADP 3PG 0.558333 0.825581
18 AMP 0.556701 0.82716
19 A 0.556701 0.82716
20 5AL 0.556604 0.841463
21 YLP 0.554622 0.872093
22 ADP VO4 0.546296 0.819277
23 SRP 0.546296 0.888889
24 VO4 ADP 0.546296 0.819277
25 LA8 ALF 3PG 0.545455 0.825581
26 ALF ADP 3PG 0.545455 0.825581
27 ADP BMA 0.544643 0.853659
28 A12 0.544554 0.821429
29 AP2 0.544554 0.821429
30 YLB 0.540984 0.872093
31 YLC 0.540984 0.892857
32 ABM 0.54 0.785714
33 A2D 0.54 0.807229
34 LAD 0.539823 0.914634
35 ADP 0.539216 0.829268
36 SRA 0.535354 0.788235
37 ME8 0.535088 0.827586
38 APC 0.533333 0.821429
39 8QN 0.531532 0.841463
40 BA3 0.529412 0.807229
41 AU1 0.528846 0.809524
42 YLA 0.528 0.872093
43 4AD 0.526786 0.878049
44 AMO 0.526786 0.865854
45 PAJ 0.526786 0.804598
46 9SN 0.525862 0.793103
47 B4P 0.524272 0.807229
48 AP5 0.524272 0.807229
49 AYB 0.52381 0.862069
50 PTJ 0.521739 0.813953
51 NB8 0.521739 0.835294
52 IOT 0.52 0.951807
53 AN2 0.519231 0.819277
54 ADX 0.514286 0.736264
55 M33 0.514286 0.797619
56 RBY 0.514019 0.821429
57 ADV 0.514019 0.821429
58 A A 0.513043 0.829268
59 AMP DBH 0.512605 0.809524
60 ATP 0.509434 0.829268
61 50T 0.509434 0.797619
62 ACP 0.509434 0.831325
63 NVA LMS 0.508772 0.736842
64 AHX 0.508772 0.835294
65 DLL 0.508772 0.841463
66 TXA 0.508621 0.821429
67 AHZ 0.508197 0.806818
68 YLY 0.507576 0.862069
69 SON 0.504762 0.865854
70 AQP 0.504673 0.829268
71 PRX 0.504673 0.788235
72 APR 0.504673 0.829268
73 5FA 0.504673 0.829268
74 AR6 0.504673 0.829268
75 ACQ 0.504587 0.831325
76 ANP 0.504587 0.809524
77 OOB 0.504425 0.841463
78 3UK 0.504348 0.831325
79 XAH 0.504202 0.870588
80 AGS 0.5 0.790698
81 WAQ 0.5 0.86747
82 SAP 0.5 0.790698
83 AD9 0.5 0.809524
84 YAP 0.495798 0.855422
85 ATP A A A 0.495798 0.839506
86 FA5 0.495798 0.865854
87 1ZZ 0.495726 0.806818
88 00A 0.495652 0.802326
89 ATF 0.495495 0.8
90 AR6 AR6 0.491803 0.851852
91 LEU LMS 0.491379 0.71875
92 TAT 0.490909 0.8
93 PR8 0.487179 0.903614
94 A1R 0.486957 0.845238
95 N0B 0.485294 0.872093
96 NAD IBO 0.484615 0.811765
97 TYM 0.484127 0.865854
98 LAQ 0.483871 0.806818
99 FYA 0.483051 0.819277
100 TSB 0.482456 0.712766
101 MAP 0.482456 0.790698
102 A5A 0.482143 0.72043
103 G5A 0.481818 0.771739
104 5AS 0.481132 0.715789
105 7MD 0.479675 0.892857
106 OAD 0.478632 0.831325
107 5SV 0.478261 0.772727
108 SSA 0.477876 0.752688
109 GJV 0.47619 0.875
110 KAA 0.474576 0.784946
111 GSU 0.474576 0.771739
112 AMP NAD 0.474453 0.843373
113 ADQ 0.474138 0.831325
114 52H 0.473684 0.697917
115 54H 0.473684 0.705263
116 VMS 0.473684 0.705263
117 JB6 0.470588 0.802326
118 3OD 0.470588 0.831325
119 BIS 0.470588 0.823529
120 NAE 0.470588 0.811765
121 NAJ PZO 0.470149 0.793103
122 NAD 0.469697 0.841463
123 53H 0.469565 0.697917
124 A22 0.469565 0.819277
125 5CA 0.469565 0.752688
126 25A 0.465517 0.829268
127 TAD 0.464 0.784091
128 4UV 0.463415 0.811765
129 A3D 0.462687 0.831325
130 P5A 0.462185 0.776596
131 DSZ 0.461538 0.752688
132 6RE 0.461538 0.8625
133 LSS 0.461538 0.71875
134 NSS 0.461538 0.752688
135 COD 0.458647 0.822222
136 7MC 0.457364 0.872093
137 AOC 0.457143 0.722892
138 48N 0.456693 0.857143
139 NAQ 0.456522 0.793103
140 NAJ PYZ 0.456522 0.775281
141 4UU 0.456 0.811765
142 ZID 0.453237 0.831325
143 J7C 0.45283 0.85
144 THR ARG SER GLY FZN VAL MET ARG ARG LEU 0.451977 0.831579
145 5CD 0.44898 0.707317
146 RAB 0.447917 0.740741
147 XYA 0.447917 0.740741
148 ADN 0.447917 0.740741
149 3DH 0.446602 0.682353
150 DTA 0.445545 0.694118
151 NDE 0.444444 0.843373
152 AFH 0.444444 0.804598
153 YSA 0.443548 0.734043
154 25L 0.442623 0.819277
155 SAH 0.442478 0.759036
156 NAI 0.44186 0.781609
157 TXD 0.44186 0.802326
158 6V0 0.44186 0.793103
159 NXX 0.44186 0.843373
160 4UW 0.44186 0.784091
161 DND 0.44186 0.843373
162 5X8 0.441441 0.756098
163 SMM 0.439655 0.722222
164 5N5 0.438776 0.740741
165 SAM 0.438596 0.727273
166 OMR 0.438462 0.797753
167 TXE 0.438462 0.802326
168 WSA 0.438462 0.741935
169 4TA 0.437037 0.797753
170 G A A A 0.437037 0.902439
171 G3A 0.436508 0.857143
172 ADJ 0.43609 0.797753
173 AP0 0.435115 0.752809
174 EEM 0.434783 0.727273
175 A4D 0.434343 0.719512
176 BT5 0.433824 0.840909
177 U A G G 0.433824 0.890244
178 G5P 0.433071 0.857143
179 NAX 0.430769 0.816092
180 SFG 0.428571 0.765432
181 NDC 0.428571 0.835294
182 MTA 0.427184 0.682353
183 A3N 0.425926 0.714286
184 CNA 0.422222 0.843373
185 EP4 0.421569 0.686047
186 M24 0.421429 0.775281
187 DAL FAD PER 0.421384 0.840909
188 SA8 0.421053 0.744186
189 UP5 0.419847 0.790698
190 Z5A 0.41958 0.771739
191 FB0 0.418919 0.815217
192 GTA 0.418605 0.848837
193 A3P 0.418182 0.82716
194 PO4 PO4 A A A A PO4 0.418033 0.814815
195 A A A 0.418033 0.841463
196 M2T 0.417476 0.670455
197 SAI 0.417391 0.75
198 DSH 0.416667 0.761905
199 GEK 0.416667 0.77381
200 A3G 0.416667 0.790123
201 A3T 0.415929 0.743902
202 S7M 0.415254 0.727273
203 139 0.414815 0.795455
204 6IA 0.413793 0.825581
205 4TC 0.413534 0.793103
206 UPA 0.413534 0.802326
207 0UM 0.413223 0.776471
208 DZD 0.413043 0.804598
209 A7D 0.410714 0.746988
210 A3S 0.410714 0.777778
211 A U 0.410448 0.833333
212 A4P 0.410448 0.852273
213 7D5 0.409524 0.77381
214 S4M 0.409091 0.722222
215 NAD BBN 0.409091 0.788889
216 PAP 0.408696 0.817073
217 4YB 0.407692 0.755319
218 MHZ 0.40708 0.714286
219 K15 0.406504 0.738636
220 649 0.406015 0.739583
221 BTX 0.405797 0.829545
222 A2P 0.405405 0.814815
223 T5A 0.404412 0.769231
224 NAD CJ3 0.403846 0.763441
225 NEC 0.40367 0.698795
226 CNV FAD 0.402516 0.804348
227 3AM 0.401869 0.814815
228 V3L 0.401709 0.851852
229 SXZ 0.4 0.727273
230 2A5 0.4 0.831325
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D57; Ligand: ARG AMP; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 4d57.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3EXS 5RP 0.01283 0.42742 1.35747
2 3LTW HLZ 0.04392 0.40624 2.14286
3 2Y4O DLL 0.000000003926 0.54688 2.48307
4 4KBA 1QM 0.01393 0.42977 3.92749
5 4BG4 ARG 0.03312 0.41371 3.93258
6 2YPI PGA 0.02415 0.4132 4.04858
7 4OEV OXL 0.04443 0.4086 4.25101
8 3A6T 8OG 0.02392 0.40307 4.65116
9 1QD0 RR6 0.03603 0.40416 6.25
10 2X1L ADN 0.0406 0.40505 6.87023
11 2Y4N DLL 0.0000002196 0.51935 11.6705
12 2Y4N PAC 0.000001547 0.45886 11.6705
13 5MST FUM 0.00000004385 0.51435 25.4799
14 5MST AMP 0.000000006798 0.50223 25.4799
15 5MSD BEZ 0.000000002565 0.5283 28.0977
16 5MSD AMP 0.000000008425 0.49026 28.0977
17 5HM3 649 0.0000007796 0.54644 28.4468
18 5EY9 5SV 0.000001143 0.48271 28.9703
19 3KXW 1ZZ 0.00000002741 0.53597 32.1117
20 5D6J ATP 0.00002036 0.41753 32.2862
21 5OE4 3UK 0.00000001859 0.66218 36.3636
22 1PG4 COA 0.00000008662 0.5046 37.1728
23 1PG4 PRX 0.00000008662 0.5046 37.1728
24 3IES M24 0.00000005745 0.56051 38.657
25 1MDB AMP DBH 0.00000004727 0.49334 39.5176
26 2D1S SLU 0.00000001834 0.55872 39.5985
27 3C5E ATP 0.00000008794 0.58329 40.1754
28 4FUT ATP 0.0000006585 0.4572 40.7555
29 1V25 ANP 0.000000006789 0.60303 41.22
30 5BSR COA 0.000000007386 0.62804 41.6974
31 5BSR AMP 0.00000001557 0.59613 41.6974
32 4GXQ ATP 0.0000001724 0.47949 41.6996
33 4RLQ 3SK 0.0000003957 0.50754 42.0039
34 4DG8 AMP 0.0000000001409 0.52709 42.0593
35 3O84 HTJ 0.000002093 0.54912 42.4632
36 5X8G S0N 0.000000001884 0.6416 43.0928
37 3NYQ AMP 0.00000001062 0.5812 43.5644
38 3NYQ MCA 0.0000000127 0.57335 43.5644
39 3CW9 AMP 0.000000005216 0.71305 43.8492
40 3CW9 01A 0.0004919 0.44488 43.8492
41 4OXI GAP 0.00000000000008682 0.6494 44.2708
42 5IE3 OXD 0.000000254 0.51542 44.358
43 5IE3 AMP 0.000000254 0.51542 44.358
44 5C5H 4YB 0.00000004074 0.53236 45.4746
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