Receptor
PDB id Resolution Class Description Source Keywords
4CH6 2.05 Å EC: 6.1.1.26 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED PROPARGYLOXYCARBONYL LYSINE METHANOSARCINA MAZEI LIGASE NON-NATURAL AMINO ACID PYRROLYSINE
Ref.: STRUCTURAL BASIS FOR THE SITE-SPECIFIC INCORPORATIO LYSINE DERIVATIVES INTO PROTEINS. PLOS ONE V. 9E96198 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1456;
A:1458;
A:1459;
A:1460;
A:1457;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
YLA A:500;
Valid;
none;
submit data
557.451 C20 H28 N7 O10 P C#CCO...
MG A:1455;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6AAD 1.44 Å EC: 6.1.1.26 CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) WITH MTMDZLYS METHANOSARCINA MAZEI JCM 9314 AMINOACYL-TRNA SYNTHETASE NON-NATURAL AMINO ACIDS TRANSLAT
Ref.: STRUCTURAL BASIS FOR GENETIC-CODE EXPANSION WITH BU LYSINE DERIVATIVES BY AN ENGINEERED PYRROLYSYL-TRNA SYNTHETASE. CELL CHEM BIOL V. 26 936 2019
Members (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6ABL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
3 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
4 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
5 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
7 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 6AAQ Kd = 3.9 mM 9U9 C17 H26 N2 O4 C1C[C@@H]2....
9 6AAO Kd = 7.8 mM 9U0 C15 H26 N2 O4 C1CCC=CC(C....
10 6AAP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
12 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
13 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
14 6AB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
16 6ABM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 4CS3 - AMP LYS FU0 n/a n/a
19 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
20 6AAN Kd = 1.76 mM 9TX C16 H20 N2 O4 C#Cc1cccc(....
21 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
22 6AB1 - 9V0 C14 H19 N5 O4 c1ccc(c(c1....
23 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
24 6ABK Kd = 11.3 mM 9VF C11 H24 N2 O4 Si C[Si](C)(C....
25 6AAC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
26 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
27 6AB0 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
28 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
30 6AAD Kd = 1.62 mM 9TU C16 H19 F3 N4 O4 c1cc(cc(c1....
31 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
32 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
33 2ZCE - PYL C12 H21 N3 O3 C[C@@H]1CC....
34 6AAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
35 6AB8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6ABL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
3 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
4 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
5 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
7 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 6AAQ Kd = 3.9 mM 9U9 C17 H26 N2 O4 C1C[C@@H]2....
9 6AAO Kd = 7.8 mM 9U0 C15 H26 N2 O4 C1CCC=CC(C....
10 6AAP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
12 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
13 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
14 6AB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
16 6ABM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 4CS3 - AMP LYS FU0 n/a n/a
19 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
20 6AAN Kd = 1.76 mM 9TX C16 H20 N2 O4 C#Cc1cccc(....
21 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
22 6AB1 - 9V0 C14 H19 N5 O4 c1ccc(c(c1....
23 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
24 6ABK Kd = 11.3 mM 9VF C11 H24 N2 O4 Si C[Si](C)(C....
25 6AAC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
26 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
27 6AB0 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
28 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
30 6AAD Kd = 1.62 mM 9TU C16 H19 F3 N4 O4 c1cc(cc(c1....
31 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
32 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
33 2ZCE - PYL C12 H21 N3 O3 C[C@@H]1CC....
34 6AAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
35 6AB8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6ABL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
3 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
4 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
5 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
7 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 6AAQ Kd = 3.9 mM 9U9 C17 H26 N2 O4 C1C[C@@H]2....
9 6AAO Kd = 7.8 mM 9U0 C15 H26 N2 O4 C1CCC=CC(C....
10 6AAP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
12 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
13 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
14 6AB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
16 6ABM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 4CS3 - AMP LYS FU0 n/a n/a
19 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
20 6AAN Kd = 1.76 mM 9TX C16 H20 N2 O4 C#Cc1cccc(....
21 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
22 6AB1 - 9V0 C14 H19 N5 O4 c1ccc(c(c1....
23 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
24 6ABK Kd = 11.3 mM 9VF C11 H24 N2 O4 Si C[Si](C)(C....
25 6AAC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
26 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
27 6AB0 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
28 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
30 6AAD Kd = 1.62 mM 9TU C16 H19 F3 N4 O4 c1cc(cc(c1....
31 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
32 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
33 2ZCE - PYL C12 H21 N3 O3 C[C@@H]1CC....
34 6AAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
35 6AB8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YLA; Similar ligands found: 239
No: Ligand ECFP6 Tc MDL keys Tc
1 YLA 1 1
2 AYB 0.825688 0.940476
3 YLP 0.777778 0.928571
4 YLC 0.756757 0.951219
5 YLB 0.756757 0.928571
6 N0B 0.756303 0.97561
7 LAD 0.740385 0.950617
8 YLY 0.702479 0.917647
9 SRP 0.673077 0.901235
10 ME8 0.654545 0.83908
11 AMO 0.648148 0.878049
12 NB8 0.63964 0.847059
13 5AL 0.638095 0.853659
14 CA0 0.61165 0.865854
15 8LH 0.611111 0.855422
16 8QN 0.609091 0.853659
17 YAP 0.608696 0.86747
18 FA5 0.608696 0.878049
19 4AD 0.603604 0.86747
20 KG4 0.590476 0.843373
21 PAJ 0.589286 0.816092
22 8LQ 0.585586 0.855422
23 PTJ 0.582609 0.804598
24 XAH 0.576271 0.904762
25 TXA 0.568965 0.855422
26 TYM 0.564516 0.878049
27 8LE 0.563636 0.823529
28 A2D 0.563107 0.819277
29 F2R 0.5625 0.883721
30 AN2 0.556604 0.809524
31 AHX 0.556522 0.847059
32 DLL 0.556522 0.853659
33 OOB 0.552632 0.853659
34 BA3 0.552381 0.819277
35 M33 0.551402 0.809524
36 ADP 0.54717 0.819277
37 AP5 0.54717 0.819277
38 B4P 0.54717 0.819277
39 WAQ 0.547009 0.925926
40 B5V 0.547009 0.833333
41 00A 0.543103 0.813953
42 AT4 0.542056 0.790698
43 PRX 0.541284 0.821429
44 ANP 0.540541 0.8
45 IOT 0.539062 0.917647
46 3UK 0.538462 0.843373
47 AU1 0.537037 0.8
48 ADX 0.537037 0.747253
49 A 0.533981 0.817073
50 AMP 0.533981 0.817073
51 9SN 0.533333 0.804598
52 45A 0.533333 0.797619
53 ABM 0.533333 0.797619
54 ATP 0.53211 0.819277
55 ACP 0.53211 0.821429
56 HEJ 0.53211 0.819277
57 50T 0.53211 0.788235
58 1ZZ 0.529412 0.860465
59 APR 0.527273 0.841463
60 AR6 0.527273 0.841463
61 AQP 0.527273 0.819277
62 5FA 0.527273 0.819277
63 9ZD 0.525862 0.813953
64 9ZA 0.525862 0.813953
65 ARG AMP 0.524194 0.872093
66 AD9 0.522523 0.8
67 SAP 0.522523 0.781609
68 AGS 0.522523 0.781609
69 A1R 0.521368 0.902439
70 PR8 0.521008 0.962963
71 DAL AMP 0.517241 0.831325
72 FYA 0.516667 0.853659
73 B5Y 0.516393 0.823529
74 ACQ 0.513274 0.821429
75 5SV 0.512821 0.825581
76 AP2 0.509259 0.833333
77 A12 0.509259 0.833333
78 ATF 0.504348 0.790698
79 3OD 0.504132 0.843373
80 B5M 0.504065 0.823529
81 SON 0.5 0.878049
82 SRA 0.5 0.77907
83 OZV 0.5 0.819277
84 GAP 0.5 0.865854
85 4UU 0.5 0.845238
86 OAD 0.5 0.843373
87 6YZ 0.5 0.821429
88 NAI 0.496124 0.813953
89 4UV 0.496 0.845238
90 ADQ 0.495798 0.843373
91 HQG 0.495726 0.831325
92 AOC 0.495327 0.756098
93 LAQ 0.492188 0.860465
94 A22 0.491525 0.809524
95 9X8 0.487603 0.802326
96 25A 0.487395 0.819277
97 TAT 0.486957 0.790698
98 T99 0.486957 0.790698
99 APC 0.486726 0.833333
100 ADP MG 0.486486 0.817073
101 4UW 0.484615 0.816092
102 KAA 0.483607 0.815217
103 A3R 0.483333 0.902439
104 ADV 0.482456 0.855422
105 RBY 0.482456 0.855422
106 80F 0.481752 0.820225
107 G3A 0.480315 0.784091
108 BIS 0.479675 0.813953
109 MAP 0.478992 0.781609
110 7MD 0.476562 0.927711
111 G5P 0.476562 0.784091
112 AFH 0.476562 0.816092
113 TXD 0.473282 0.857143
114 DQV 0.472868 0.831325
115 M24 0.471429 0.786517
116 ADP PO3 0.469565 0.817073
117 APC MG 0.469565 0.819277
118 ATP MG 0.469565 0.817073
119 COD 0.467153 0.875
120 48N 0.465649 0.825581
121 MYR AMP 0.464 0.83908
122 25L 0.464 0.809524
123 BT5 0.463768 0.873563
124 SSA 0.462185 0.763441
125 NAX 0.462121 0.848837
126 NXX 0.462121 0.833333
127 DND 0.462121 0.833333
128 TYR AMP 0.460938 0.845238
129 GJV 0.459459 0.755814
130 6RE 0.458716 0.744186
131 OMR 0.458647 0.850575
132 TXE 0.458647 0.857143
133 JB6 0.456 0.835294
134 ADJ 0.455882 0.872093
135 AP0 0.455224 0.784091
136 5CA 0.454545 0.763441
137 TSB 0.454545 0.723404
138 53H 0.454545 0.708333
139 GA7 0.453846 0.811765
140 A5A 0.453782 0.731183
141 ADP ALF 0.453782 0.761364
142 ALF ADP 0.453782 0.761364
143 6V0 0.451128 0.825581
144 A3N 0.45045 0.746988
145 J7C 0.45045 0.752941
146 GTA 0.450382 0.758242
147 ADP VO4 0.45 0.809524
148 VO4 ADP 0.45 0.809524
149 AMP DBH 0.449612 0.77907
150 LMS 0.449541 0.728261
151 GSU 0.448 0.782609
152 LSS 0.447154 0.729167
153 DSZ 0.447154 0.763441
154 54H 0.446281 0.715789
155 NO7 0.446281 0.855422
156 VMS 0.446281 0.715789
157 G5A 0.440678 0.782609
158 SAI 0.440678 0.761905
159 ADP BMA 0.44 0.821429
160 SFG 0.439655 0.777778
161 TAD 0.439394 0.816092
162 5AS 0.438596 0.744681
163 SMM 0.438017 0.714286
164 AF3 ADP 3PG 0.437037 0.795455
165 J4G 0.436508 0.890244
166 BTX 0.435714 0.862069
167 NAQ 0.434483 0.784091
168 52H 0.434426 0.708333
169 7MC 0.433824 0.905882
170 8Q2 0.433824 0.757895
171 LPA AMP 0.432836 0.83908
172 SA8 0.432203 0.755814
173 NVA LMS 0.432 0.739583
174 CNA 0.431655 0.833333
175 8X1 0.430894 0.776596
176 YSA 0.430769 0.744681
177 A4P 0.430657 0.802198
178 UP5 0.42963 0.823529
179 K15 0.428571 0.770115
180 FB0 0.427632 0.846154
181 NAE 0.427586 0.802326
182 5X8 0.42735 0.746988
183 EAD 0.425676 0.806818
184 NAD 0.425532 0.831325
185 AHZ 0.425373 0.777778
186 P5A 0.425197 0.826087
187 A A 0.425197 0.797619
188 T5A 0.42446 0.840909
189 0UM 0.424 0.809524
190 NSS 0.424 0.744681
191 NDE 0.423841 0.811765
192 2A5 0.423729 0.843373
193 4TC 0.423358 0.825581
194 UPA 0.423358 0.835294
195 ZID 0.421769 0.821429
196 EEM 0.421488 0.719101
197 62X 0.420635 0.752809
198 PAP 0.420168 0.807229
199 A3D 0.41958 0.821429
200 5CD 0.419048 0.698795
201 ADN 0.417476 0.731707
202 XYA 0.417476 0.731707
203 RAB 0.417476 0.731707
204 LEU LMS 0.417323 0.721649
205 NAJ PZO 0.416667 0.784091
206 SAH 0.416667 0.771084
207 0WD 0.415493 0.804598
208 S7M 0.414634 0.719101
209 139 0.414286 0.870588
210 SAM 0.413223 0.719101
211 ATP A 0.412214 0.807229
212 ATP A A A 0.412214 0.807229
213 8PZ 0.412214 0.744681
214 9K8 0.410853 0.67
215 A3S 0.410256 0.768293
216 PPS 0.409836 0.728261
217 5N5 0.409524 0.731707
218 7D5 0.409091 0.785714
219 NDC 0.409091 0.869048
220 7D3 0.408696 0.788235
221 ATR 0.408333 0.795181
222 EP4 0.407407 0.678161
223 KH3 0.407407 0.781609
224 7D4 0.40678 0.788235
225 WSA 0.405797 0.752688
226 A4D 0.40566 0.710843
227 AMP NAD 0.405594 0.831325
228 3DH 0.405405 0.674419
229 NAJ PYZ 0.405405 0.75
230 P1H 0.405229 0.808989
231 A3P 0.405172 0.817073
232 DTA 0.40367 0.705882
233 H1Q 0.403361 0.785714
234 DZD 0.402778 0.858824
235 6IA 0.401639 0.816092
236 OZP 0.40146 0.819277
237 AR6 AR6 0.4 0.819277
238 MTA 0.4 0.674419
239 A2R 0.4 0.831325
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6AAD; Ligand: 9TU; Similar sites found with APoc: 17
This union binding pocket(no: 1) in the query (biounit: 6aad.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 1X54 4AD 7.29927
2 2XGT NSS 9.12409
3 2XGT NSS 9.12409
4 6AGT 9X0 14.9635
5 6AGT 9X0 14.9635
6 3G1Z AMP 16.7883
7 3G1Z AMP 16.7883
8 3A5Y KAA 17.1533
9 3A5Y KAA 17.1533
10 3A5Z KAA 17.1533
11 3A5Z KAA 17.1533
12 3REU ATP 17.5182
13 3REU ATP 17.5182
14 3NEM ATP 18.2482
15 3NEM AMO 18.2482
16 3E9I XAH 22.2628
17 3E9I XAH 22.2628
Pocket No.: 2; Query (leader) PDB : 6AAD; Ligand: 9TU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6aad.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6AAD; Ligand: ATP; Similar sites found with APoc: 17
This union binding pocket(no: 3) in the query (biounit: 6aad.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 1X54 4AD 7.29927
2 2XGT NSS 9.12409
3 2XGT NSS 9.12409
4 6AGT 9X0 14.9635
5 6AGT 9X0 14.9635
6 3G1Z AMP 16.7883
7 3G1Z AMP 16.7883
8 3A5Y KAA 17.1533
9 3A5Y KAA 17.1533
10 3A5Z KAA 17.1533
11 3A5Z KAA 17.1533
12 3REU ATP 17.5182
13 3REU ATP 17.5182
14 3NEM ATP 18.2482
15 3NEM AMO 18.2482
16 3E9I XAH 22.2628
17 3E9I XAH 22.2628
Pocket No.: 4; Query (leader) PDB : 6AAD; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6aad.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
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