Receptor
PDB id Resolution Class Description Source Keywords
4CH3 2.28 Å EC: 6.1.1.26 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED BUTYRYL 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)...
YLB A:500;
Valid;
none;
submit data
545.483 C20 H32 N7 O9 P CCCC(...
MG A:1455;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CS4 1.35 Å EC: 6.1.1.26 CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE MUTANT Y306A, Y384F IN COMPLEX WITH AMPPNP METHANOSARCINA MAZEI LIGASE AMINOACYL-TRNA SYNTHETASE NONCANONICAL AMINO ACIDS
Ref.: STRUCTURAL BASIS OF FURAN-AMINO ACID RECOGNITION BY POLYSPECIFIC AMINOACYL-TRNA-SYNTHETASE AND ITS GENE ENCODING IN HUMAN CELLS. CHEMBIOCHEM V. 15 1755 2014
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
2 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
4 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
7 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
8 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
9 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
10 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
11 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
12 4CS3 - AMP LYS FU0 n/a n/a
13 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
14 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
15 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
17 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
19 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
20 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
21 2ZCE - PYH C12 H21 N3 O3 C[C@@H]1CC....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
2 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
4 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
7 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
8 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
9 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
10 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
11 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
12 4CS3 - AMP LYS FU0 n/a n/a
13 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
14 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
15 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
17 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
19 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
20 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
21 2ZCE - PYH C12 H21 N3 O3 C[C@@H]1CC....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
2 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
4 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
7 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
8 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
9 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
10 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
11 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
12 4CS3 - AMP LYS FU0 n/a n/a
13 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
14 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
15 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
17 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
19 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
20 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
21 2ZCE - PYH C12 H21 N3 O3 C[C@@H]1CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YLB; Similar ligands found: 300
No: Ligand ECFP6 Tc MDL keys Tc
1 YLB 1 1
2 YLP 0.871287 0.97561
3 AYB 0.798165 0.987805
4 YLC 0.794393 0.951219
5 LAD 0.762376 0.950617
6 YLA 0.756757 0.928571
7 YLY 0.735043 0.963855
8 N0B 0.702479 0.928571
9 SRP 0.693069 0.901235
10 ME8 0.688679 0.882353
11 5AL 0.673267 0.876543
12 NB8 0.672897 0.847059
13 AMO 0.666667 0.878049
14 4AD 0.650943 0.86747
15 8QN 0.641509 0.876543
16 YAP 0.63964 0.86747
17 CA0 0.63 0.843373
18 FA5 0.625 0.878049
19 PAJ 0.62037 0.858824
20 PRX 0.601942 0.888889
21 1ZZ 0.598214 0.927711
22 PTJ 0.598214 0.847059
23 XAH 0.591304 0.904762
24 WAQ 0.589286 0.925926
25 M33 0.582524 0.831325
26 A2D 0.58 0.819277
27 TYM 0.578512 0.878049
28 F2R 0.576 0.883721
29 AN2 0.572816 0.809524
30 AHX 0.571429 0.847059
31 DLL 0.571429 0.853659
32 TXA 0.570175 0.855422
33 BA3 0.568627 0.819277
34 5SV 0.567568 0.891566
35 SAP 0.566038 0.781609
36 AGS 0.566038 0.781609
37 ABM 0.564356 0.819277
38 ADP 0.563107 0.819277
39 B4P 0.563107 0.819277
40 AP5 0.563107 0.819277
41 AT4 0.557692 0.790698
42 ANP 0.555556 0.8
43 OOB 0.553571 0.853659
44 3UK 0.552632 0.843373
45 ADX 0.552381 0.747253
46 IOT 0.552 0.917647
47 ARG AMP 0.55 0.872093
48 AMP 0.55 0.817073
49 A 0.55 0.817073
50 B5V 0.547826 0.833333
51 ATP 0.54717 0.819277
52 HEJ 0.54717 0.819277
53 ACP 0.54717 0.821429
54 50T 0.54717 0.788235
55 9SN 0.547009 0.804598
56 SRA 0.544554 0.77907
57 00A 0.54386 0.813953
58 B5Y 0.542373 0.845238
59 APR 0.542056 0.841463
60 AQP 0.542056 0.819277
61 AR6 0.542056 0.841463
62 5FA 0.542056 0.819277
63 9ZD 0.539823 0.835294
64 9ZA 0.539823 0.835294
65 OAD 0.53913 0.865854
66 AU1 0.537736 0.8
67 AD9 0.537037 0.8
68 A1R 0.535088 0.902439
69 PR8 0.534483 0.962963
70 DAL AMP 0.530973 0.853659
71 FYA 0.529915 0.853659
72 3OD 0.529915 0.865854
73 B5M 0.529412 0.845238
74 OMR 0.528 0.916667
75 ACQ 0.527273 0.821429
76 9X8 0.525862 0.823529
77 MYR AMP 0.525424 0.904762
78 A12 0.52381 0.833333
79 AP2 0.52381 0.833333
80 COD 0.523077 0.918605
81 NAI 0.52 0.793103
82 ATF 0.517857 0.790698
83 LAQ 0.516129 0.860465
84 SON 0.514019 0.878049
85 GAP 0.513514 0.865854
86 6YZ 0.513274 0.821429
87 4UU 0.512195 0.823529
88 4UV 0.508197 0.823529
89 4UW 0.507937 0.816092
90 A22 0.504348 0.809524
91 BIS 0.504202 0.813953
92 TAT 0.5 0.790698
93 25A 0.5 0.819277
94 T99 0.5 0.790698
95 7MD 0.5 0.927711
96 APC 0.5 0.833333
97 TYR AMP 0.495935 0.845238
98 KAA 0.495798 0.815217
99 ADQ 0.495726 0.843373
100 A3R 0.495726 0.902439
101 ADV 0.495495 0.855422
102 RBY 0.495495 0.855422
103 ADP PO3 0.495495 0.817073
104 G3A 0.491935 0.784091
105 MAP 0.491379 0.781609
106 AP0 0.488372 0.784091
107 48N 0.488189 0.847059
108 G5P 0.488 0.784091
109 BT5 0.485075 0.873563
110 M24 0.481752 0.786517
111 80F 0.481481 0.8
112 TXE 0.48062 0.835294
113 NVA LMS 0.478992 0.795699
114 TSB 0.478632 0.741935
115 A5A 0.478261 0.75
116 5AS 0.477064 0.782609
117 J7C 0.476636 0.752941
118 GA7 0.47619 0.855422
119 AFH 0.47619 0.816092
120 25L 0.47541 0.809524
121 K15 0.475 0.833333
122 SMM 0.474138 0.752809
123 SSA 0.474138 0.763441
124 6V0 0.472868 0.804598
125 TXD 0.472868 0.835294
126 NAX 0.472868 0.827586
127 DQV 0.472441 0.831325
128 GTA 0.472441 0.777778
129 GJV 0.472222 0.755814
130 6RE 0.471698 0.744186
131 GSU 0.471074 0.782609
132 LSS 0.470588 0.765957
133 VMS 0.470085 0.734043
134 54H 0.470085 0.734043
135 SA8 0.469027 0.797619
136 JB6 0.467213 0.835294
137 5CA 0.466102 0.763441
138 53H 0.466102 0.726316
139 7MC 0.465649 0.928571
140 ADP ALF 0.465517 0.761364
141 ALF ADP 0.465517 0.761364
142 G5A 0.464912 0.782609
143 LMS 0.462264 0.728261
144 DND 0.461538 0.833333
145 NXX 0.461538 0.833333
146 ADP VO4 0.461538 0.809524
147 VO4 ADP 0.461538 0.809524
148 AMP DBH 0.460317 0.77907
149 0UM 0.458333 0.876543
150 DSZ 0.458333 0.763441
151 NSS 0.458333 0.744681
152 52H 0.457627 0.726316
153 EEM 0.456897 0.758621
154 FB0 0.455782 0.88764
155 CAJ 0.455782 0.931035
156 NAQ 0.453901 0.825581
157 LPA AMP 0.453846 0.83908
158 AOC 0.453704 0.714286
159 YSA 0.452381 0.744681
160 CA6 0.452055 0.806122
161 CNA 0.451852 0.833333
162 LEU LMS 0.45082 0.757895
163 UP5 0.450382 0.802326
164 KH3 0.449612 0.845238
165 TAD 0.449612 0.816092
166 S7M 0.449153 0.758621
167 SAM 0.448276 0.758621
168 AMX 0.447552 0.918605
169 0T1 0.446809 0.930233
170 BTX 0.445255 0.862069
171 ADJ 0.444444 0.850575
172 T5A 0.444444 0.840909
173 CMX 0.444444 0.930233
174 UPA 0.443609 0.813953
175 4TC 0.443609 0.804598
176 3DH 0.443396 0.714286
177 DCA 0.442857 0.908046
178 62X 0.442623 0.793103
179 ARU 0.442623 0.775281
180 SAI 0.439655 0.761905
181 NMX 0.439189 0.840426
182 ADP BMA 0.439024 0.821429
183 A3D 0.438849 0.843373
184 5X8 0.438596 0.746988
185 SFG 0.438596 0.777778
186 HAX 0.438356 0.88764
187 NAE 0.43662 0.845238
188 AF3 ADP 3PG 0.43609 0.795455
189 6IA 0.435897 0.858824
190 A A 0.435484 0.797619
191 AHZ 0.435115 0.797753
192 NAD 0.434783 0.831325
193 2A5 0.434783 0.843373
194 0WD 0.434783 0.784091
195 EAD 0.434483 0.827586
196 CA8 0.434211 0.806122
197 139 0.433824 0.848837
198 ATP A A A 0.433071 0.807229
199 8PZ 0.433071 0.744681
200 EP4 0.432692 0.717647
201 ETB 0.432624 0.853933
202 P1H 0.432432 0.850575
203 MCD 0.432432 0.909091
204 6AD 0.432203 0.775281
205 9K8 0.432 0.704082
206 5CD 0.431373 0.698795
207 PAP 0.431034 0.807229
208 ZID 0.430556 0.821429
209 RAB 0.43 0.731707
210 XYA 0.43 0.731707
211 ADN 0.43 0.731707
212 8X1 0.429752 0.776596
213 A4P 0.42963 0.782609
214 M2T 0.428571 0.681818
215 CAO 0.427586 0.877778
216 4YB 0.427481 0.765957
217 SAH 0.42735 0.771084
218 SCD 0.426667 0.930233
219 COA 0.426573 0.908046
220 P5A 0.424 0.826087
221 BCO 0.423841 0.909091
222 FCX 0.421769 0.898876
223 FAM 0.421769 0.88764
224 5N5 0.421569 0.731707
225 A3S 0.421053 0.768293
226 7D5 0.420561 0.785714
227 PPS 0.420168 0.728261
228 AR6 AR6 0.419847 0.819277
229 7D3 0.419643 0.788235
230 S4M 0.419643 0.772727
231 HXC 0.419355 0.888889
232 ATR 0.418803 0.795181
233 30N 0.417808 0.831579
234 COS 0.417808 0.88764
235 0ET 0.417722 0.888889
236 A4D 0.417476 0.710843
237 7D4 0.417391 0.788235
238 MHZ 0.417391 0.804598
239 P5F 0.417178 0.804348
240 MAO 0.415929 0.804598
241 A3P 0.415929 0.817073
242 NAJ PZO 0.415493 0.764045
243 VRT 0.415254 0.817073
244 DTA 0.415094 0.705882
245 SCO 0.414966 0.930233
246 WSA 0.414815 0.752688
247 GEK 0.414634 0.764706
248 A1S 0.414474 0.88764
249 A3G 0.414414 0.780488
250 NEC 0.414414 0.731707
251 CO8 0.414013 0.888889
252 A3T 0.413793 0.756098
253 SOP 0.413333 0.88764
254 NDE 0.413333 0.811765
255 NDP 0.413043 0.784091
256 HDC 0.4125 0.888889
257 ACO 0.412162 0.877778
258 F0P 0.411765 0.819277
259 UCC 0.411392 0.888889
260 DCC 0.411392 0.888889
261 MYA 0.411392 0.888889
262 ST9 0.411392 0.888889
263 5F9 0.411392 0.888889
264 MFK 0.411392 0.888889
265 DZD 0.411348 0.858824
266 MTA 0.411215 0.714286
267 A3N 0.410714 0.705882
268 1VU 0.410596 0.898876
269 MRS 0.409938 0.888889
270 MRR 0.409938 0.888889
271 A2R 0.409836 0.831325
272 01K 0.409639 0.88764
273 2MC 0.407895 0.849462
274 NVA 2AD 0.40678 0.807229
275 FYN 0.406667 0.908046
276 3KK 0.406667 0.88764
277 3CP 0.406452 0.909091
278 KB1 0.40625 0.747126
279 IVC 0.405229 0.897727
280 3HC 0.405229 0.897727
281 ITT 0.405172 0.77381
282 649 0.404412 0.787234
283 AMP NAD 0.404255 0.831325
284 NAJ PYZ 0.40411 0.731183
285 COK 0.403974 0.88764
286 OXK 0.403974 0.909091
287 NHM 0.403727 0.888889
288 NHW 0.403727 0.888889
289 UOQ 0.403727 0.888889
290 A2P 0.403509 0.804878
291 COO 0.402597 0.88764
292 FNK 0.402516 0.806452
293 3NZ 0.401575 0.764706
294 8Q2 0.40146 0.721649
295 CO6 0.401316 0.88764
296 CMC 0.401316 0.909091
297 GRA 0.401274 0.909091
298 2CP 0.4 0.898876
299 3AM 0.4 0.804878
300 MC4 0.4 0.840426
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4CS4; Ligand: AXZ; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 4cs4.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
1 3G1Z AMP 16.7883
2 3A5Y KAA 17.1533
3 3A5Z KAA 17.1533
Pocket No.: 2; Query (leader) PDB : 4CS4; Ligand: AXZ; 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: 4cs4.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4CS4; Ligand: ANP; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 4cs4.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 3G1Z AMP 16.7883
2 3A5Y KAA 17.1533
3 3A5Z KAA 17.1533
Pocket No.: 4; Query (leader) PDB : 4CS4; Ligand: ANP; 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: 4cs4.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
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