Receptor
PDB id Resolution Class Description Source Keywords
4CH5 2.2 Å EC: 6.1.1.26 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED PROPIONYL 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
POP A:1461;
Invalid;
none;
submit data
175.959 H2 O7 P2 O[P@@...
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)...
YLP A:500;
Valid;
none;
submit data
531.457 C19 H30 N7 O9 P CCC(=...
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
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: YLP; Similar ligands found: 305
No: Ligand ECFP6 Tc MDL keys Tc
1 YLP 1 1
2 YLB 0.871287 0.97561
3 YLC 0.817308 0.951219
4 AYB 0.803738 0.963855
5 LAD 0.785714 0.950617
6 YLA 0.777778 0.928571
7 YLY 0.754386 0.963855
8 SRP 0.714286 0.901235
9 ME8 0.708738 0.860465
10 N0B 0.705882 0.928571
11 5AL 0.693878 0.876543
12 NB8 0.692308 0.847059
13 AMO 0.686275 0.878049
14 8QN 0.660194 0.876543
15 4AD 0.653846 0.86747
16 CA0 0.649485 0.843373
17 FA5 0.642202 0.878049
18 YAP 0.642202 0.86747
19 PAJ 0.638095 0.837209
20 PTJ 0.614679 0.825581
21 XAH 0.607143 0.904762
22 PRX 0.60396 0.865854
23 M33 0.6 0.831325
24 A2D 0.597938 0.819277
25 TYM 0.59322 0.878049
26 WAQ 0.590909 0.925926
27 F2R 0.590164 0.883721
28 AN2 0.59 0.809524
29 DLL 0.587156 0.853659
30 AHX 0.587156 0.847059
31 BA3 0.585859 0.819277
32 TXA 0.585586 0.855422
33 1ZZ 0.585586 0.927711
34 ABM 0.581633 0.819277
35 ADP 0.58 0.819277
36 AP5 0.58 0.819277
37 B4P 0.58 0.819277
38 AT4 0.574257 0.790698
39 ANP 0.571429 0.8
40 5SV 0.568807 0.891566
41 OOB 0.568807 0.853659
42 ADX 0.568627 0.747253
43 3UK 0.567568 0.843373
44 SAP 0.567308 0.781609
45 AGS 0.567308 0.781609
46 AMP 0.56701 0.817073
47 A 0.56701 0.817073
48 IOT 0.565574 0.917647
49 ARG AMP 0.564103 0.872093
50 50T 0.563107 0.788235
51 ACP 0.563107 0.821429
52 HEJ 0.563107 0.819277
53 ATP 0.563107 0.819277
54 B5V 0.5625 0.833333
55 9SN 0.561404 0.804598
56 00A 0.558559 0.813953
57 AQP 0.557692 0.819277
58 APR 0.557692 0.841463
59 5FA 0.557692 0.819277
60 AR6 0.557692 0.841463
61 B5Y 0.556522 0.845238
62 9ZD 0.554545 0.835294
63 9ZA 0.554545 0.835294
64 AU1 0.553398 0.8
65 AD9 0.552381 0.8
66 A1R 0.54955 0.902439
67 PR8 0.548673 0.962963
68 DAL AMP 0.545455 0.853659
69 SRA 0.545455 0.77907
70 FYA 0.54386 0.853659
71 3OD 0.54386 0.865854
72 B5M 0.543103 0.845238
73 ACQ 0.542056 0.821429
74 OAD 0.539823 0.865854
75 A12 0.539216 0.833333
76 AP2 0.539216 0.833333
77 ATF 0.53211 0.790698
78 GAP 0.527778 0.865854
79 6YZ 0.527273 0.821429
80 9X8 0.526316 0.823529
81 4UU 0.525 0.823529
82 4UV 0.521008 0.823529
83 4UW 0.520325 0.837209
84 NAI 0.520325 0.793103
85 A22 0.517857 0.809524
86 LAQ 0.516393 0.860465
87 SON 0.514286 0.878049
88 APC 0.514019 0.833333
89 T99 0.513761 0.790698
90 TAT 0.513761 0.790698
91 25A 0.513274 0.819277
92 MYR AMP 0.512821 0.904762
93 COD 0.511628 0.896552
94 ADP PO3 0.509259 0.817073
95 ADV 0.509259 0.855422
96 RBY 0.509259 0.855422
97 ADQ 0.508772 0.843373
98 A3R 0.508772 0.902439
99 KAA 0.508621 0.815217
100 MAP 0.504425 0.781609
101 BIS 0.504274 0.813953
102 G3A 0.504132 0.784091
103 OMR 0.504 0.916667
104 48N 0.5 0.869048
105 7MD 0.5 0.927711
106 AP0 0.5 0.784091
107 G5P 0.5 0.784091
108 TYR AMP 0.495868 0.845238
109 M24 0.492537 0.786517
110 80F 0.492424 0.8
111 TXE 0.492063 0.835294
112 TSB 0.491228 0.741935
113 A5A 0.491071 0.75
114 5AS 0.490566 0.782609
115 GA7 0.487805 0.833333
116 AFH 0.487805 0.816092
117 25L 0.487395 0.809524
118 SSA 0.486726 0.763441
119 VO4 ADP 0.486726 0.809524
120 ADP VO4 0.486726 0.809524
121 GJV 0.485714 0.755814
122 6RE 0.485437 0.744186
123 BT5 0.484848 0.873563
124 NAX 0.484127 0.827586
125 TXD 0.484127 0.835294
126 6V0 0.484127 0.804598
127 GTA 0.483871 0.777778
128 DQV 0.483871 0.831325
129 LSS 0.482759 0.747368
130 54H 0.482456 0.734043
131 VMS 0.482456 0.734043
132 SA8 0.481818 0.776471
133 JB6 0.478992 0.835294
134 NVA LMS 0.478632 0.776596
135 5CA 0.478261 0.763441
136 53H 0.478261 0.726316
137 ALF ADP 0.477876 0.761364
138 ADP ALF 0.477876 0.761364
139 G5A 0.477477 0.782609
140 J7C 0.47619 0.752941
141 LMS 0.475728 0.728261
142 K15 0.474576 0.833333
143 NAQ 0.474453 0.825581
144 SMM 0.473684 0.752809
145 NXX 0.472441 0.833333
146 DND 0.472441 0.833333
147 GSU 0.470588 0.782609
148 DSZ 0.470085 0.763441
149 52H 0.469565 0.726316
150 7MC 0.465116 0.951807
151 LEU LMS 0.462185 0.739583
152 CNA 0.462121 0.833333
153 UP5 0.460938 0.802326
154 S7M 0.46087 0.77907
155 TAD 0.460317 0.816092
156 AMP DBH 0.459677 0.77907
157 A A 0.458333 0.797619
158 0UM 0.457627 0.853659
159 NSS 0.457627 0.744681
160 3DH 0.456311 0.714286
161 EEM 0.45614 0.738636
162 PAP 0.455357 0.807229
163 ATP A A A 0.455285 0.807229
164 BTX 0.455224 0.862069
165 FB0 0.455172 0.88764
166 ADJ 0.454545 0.850575
167 T5A 0.454545 0.840909
168 UPA 0.453846 0.813953
169 4TC 0.453846 0.804598
170 62X 0.453782 0.793103
171 ARU 0.453782 0.775281
172 LPA AMP 0.453125 0.83908
173 AOC 0.45283 0.714286
174 YSA 0.451613 0.744681
175 SAH 0.451327 0.771084
176 SAI 0.451327 0.761905
177 5X8 0.45045 0.746988
178 SFG 0.45045 0.777778
179 ADP BMA 0.45 0.821429
180 KH3 0.448819 0.845238
181 A3D 0.448529 0.843373
182 6IA 0.447368 0.837209
183 SAM 0.447368 0.738636
184 2A5 0.446429 0.843373
185 AF3 ADP 3PG 0.446154 0.795455
186 NAE 0.446043 0.823529
187 EP4 0.445545 0.697674
188 AHZ 0.445312 0.818182
189 CAJ 0.445205 0.931035
190 0WD 0.444444 0.784091
191 NAD 0.444444 0.831325
192 5CD 0.444444 0.698795
193 EAD 0.443662 0.827586
194 139 0.443609 0.848837
195 8PZ 0.443548 0.744681
196 PPS 0.443478 0.728261
197 XYA 0.443299 0.731707
198 RAB 0.443299 0.731707
199 ADN 0.443299 0.731707
200 9K8 0.442623 0.704082
201 DCA 0.442029 0.908046
202 ETB 0.442029 0.853933
203 CA6 0.441379 0.806122
204 8X1 0.440678 0.776596
205 A3P 0.440367 0.817073
206 A4P 0.439394 0.782609
207 AMX 0.43662 0.896552
208 0T1 0.435714 0.908046
209 P5A 0.434426 0.826087
210 5N5 0.434343 0.731707
211 CMX 0.433566 0.908046
212 7D5 0.432692 0.785714
213 A3S 0.432432 0.768293
214 P1H 0.431507 0.829545
215 7D3 0.431193 0.788235
216 6AD 0.431034 0.775281
217 DZD 0.430657 0.858824
218 A4D 0.43 0.710843
219 ATR 0.429825 0.795181
220 AR6 AR6 0.429688 0.819277
221 ZID 0.429577 0.821429
222 MHZ 0.428571 0.804598
223 7D4 0.428571 0.788235
224 NMX 0.428571 0.821053
225 HAX 0.427586 0.866667
226 M2T 0.427184 0.662921
227 DTA 0.427184 0.705882
228 CAO 0.426573 0.857143
229 NEC 0.425926 0.731707
230 A3G 0.425926 0.780488
231 COA 0.425532 0.886364
232 GEK 0.425 0.764706
233 A3T 0.424779 0.756098
234 3AM 0.424528 0.804878
235 NAJ PZO 0.42446 0.764045
236 WSA 0.424242 0.752688
237 CA8 0.423841 0.787879
238 MTA 0.423077 0.694118
239 A3N 0.422018 0.705882
240 NDE 0.421769 0.811765
241 MCD 0.421769 0.909091
242 FAM 0.42069 0.866667
243 FCX 0.42069 0.877778
244 A2R 0.420168 0.831325
245 A7D 0.419643 0.759036
246 SXZ 0.419355 0.77907
247 1VU 0.418919 0.898876
248 S4M 0.418182 0.772727
249 COS 0.416667 0.866667
250 30N 0.416667 0.8125
251 SCD 0.416107 0.908046
252 ITT 0.415929 0.77381
253 4YB 0.415385 0.765957
254 A2P 0.414414 0.804878
255 MAO 0.414414 0.784091
256 VRT 0.413793 0.795181
257 SCO 0.413793 0.908046
258 A1S 0.413333 0.866667
259 A G 0.413043 0.772727
260 AMP NAD 0.413043 0.831325
261 G A A A 0.413043 0.784091
262 NAJ PYZ 0.412587 0.731183
263 SOP 0.412162 0.88764
264 NDP 0.411765 0.784091
265 ACO 0.410959 0.877778
266 8Q2 0.410448 0.721649
267 F0P 0.410448 0.819277
268 FNK 0.410256 0.787234
269 U A G G 0.410072 0.772727
270 HXC 0.409091 0.888889
271 01K 0.408537 0.88764
272 0ET 0.407643 0.888889
273 NDC 0.406667 0.869048
274 2MC 0.406667 0.849462
275 3KK 0.405405 0.88764
276 FYN 0.405405 0.886364
277 3CP 0.405229 0.88764
278 NVA 2AD 0.405172 0.785714
279 KB1 0.404762 0.747126
280 3HC 0.403974 0.876405
281 IVC 0.403974 0.876405
282 BCO 0.403974 0.88764
283 CO8 0.403846 0.888889
284 2SA 0.403361 0.855422
285 NA7 0.403226 0.855422
286 649 0.402985 0.787234
287 OXK 0.402685 0.88764
288 COK 0.402685 0.866667
289 HDC 0.402516 0.888889
290 HFD 0.401709 0.781609
291 COO 0.401316 0.866667
292 FDA 0.401316 0.793478
293 UCC 0.401274 0.888889
294 DCC 0.401274 0.888889
295 MFK 0.401274 0.888889
296 5F9 0.401274 0.888889
297 ST9 0.401274 0.888889
298 MYA 0.401274 0.888889
299 MRR 0.4 0.888889
300 GRA 0.4 0.88764
301 CO6 0.4 0.88764
302 3NZ 0.4 0.764706
303 DSH 0.4 0.795181
304 MRS 0.4 0.888889
305 CMC 0.4 0.88764
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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