Receptor
PDB id Resolution Class Description Source Keywords
4CH4 2.16 Å EC: 6.1.1.26 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED CROTONYL 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)...
YLC A:500;
Valid;
none;
submit data
543.467 C20 H30 N7 O9 P C/C=C...
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: YLC; Similar ligands found: 254
No: Ligand ECFP6 Tc MDL keys Tc
1 YLC 1 1
2 YLP 0.817308 0.951219
3 YLB 0.794393 0.951219
4 AYB 0.765766 0.939759
5 LAD 0.762376 0.974684
6 YLA 0.756757 0.951219
7 YLY 0.720339 0.939759
8 SRP 0.693069 0.924051
9 ME8 0.688679 0.880952
10 N0B 0.688525 0.951219
11 5AL 0.673267 0.898734
12 AMO 0.666667 0.9
13 NB8 0.657407 0.86747
14 8QN 0.641509 0.898734
15 YAP 0.63964 0.888889
16 CA0 0.63 0.864198
17 FA5 0.625 0.9
18 PAJ 0.62037 0.857143
19 4AD 0.62037 0.888889
20 PTJ 0.598214 0.845238
21 XAH 0.591304 0.926829
22 F2R 0.58871 0.904762
23 AN2 0.588235 0.829268
24 M33 0.582524 0.851852
25 A2D 0.58 0.839506
26 TYM 0.578512 0.9
27 DLL 0.571429 0.875
28 PRX 0.571429 0.841463
29 AHX 0.571429 0.86747
30 TXA 0.570175 0.876543
31 BA3 0.568627 0.839506
32 ADX 0.567308 0.764045
33 IOT 0.564516 0.916667
34 ABM 0.564356 0.839506
35 B4P 0.563107 0.839506
36 ADP 0.563107 0.839506
37 AP5 0.563107 0.839506
38 50T 0.561905 0.807229
39 WAQ 0.561404 0.925
40 AT4 0.557692 0.809524
41 1ZZ 0.556522 0.880952
42 ANP 0.555556 0.819277
43 OOB 0.553571 0.875
44 3UK 0.552632 0.864198
45 4UU 0.55 0.865854
46 A 0.55 0.8375
47 AMP 0.55 0.8375
48 B5V 0.547826 0.853659
49 ATP 0.54717 0.839506
50 ACP 0.54717 0.841463
51 HEJ 0.54717 0.839506
52 9SN 0.547009 0.823529
53 4UV 0.546219 0.865854
54 00A 0.54386 0.833333
55 B5Y 0.542373 0.865854
56 APR 0.542056 0.8625
57 5FA 0.542056 0.839506
58 AR6 0.542056 0.8625
59 AQP 0.542056 0.839506
60 9ZD 0.539823 0.855422
61 9ZA 0.539823 0.855422
62 5SV 0.539823 0.845238
63 AU1 0.537736 0.819277
64 ARG AMP 0.53719 0.892857
65 AD9 0.537037 0.819277
66 AGS 0.537037 0.8
67 SAP 0.537037 0.8
68 A1R 0.535088 0.901235
69 PR8 0.534483 0.9625
70 4UW 0.532258 0.857143
71 DAL AMP 0.530973 0.875
72 3OD 0.529915 0.8875
73 FYA 0.529915 0.851852
74 B5M 0.529412 0.865854
75 ACQ 0.527273 0.841463
76 OAD 0.525862 0.8875
77 AP2 0.52381 0.853659
78 A12 0.52381 0.853659
79 ATF 0.517857 0.809524
80 SRA 0.514563 0.797619
81 SON 0.514019 0.9
82 GAP 0.513514 0.8875
83 6YZ 0.513274 0.841463
84 9X8 0.512821 0.843373
85 48N 0.512 0.86747
86 NAI 0.507937 0.833333
87 A22 0.504348 0.829268
88 LAQ 0.504 0.858824
89 T99 0.5 0.809524
90 25A 0.5 0.839506
91 APC 0.5 0.853659
92 TAT 0.5 0.809524
93 KAA 0.495798 0.833333
94 ADQ 0.495726 0.864198
95 A3R 0.495726 0.901235
96 RBY 0.495495 0.876543
97 ADV 0.495495 0.876543
98 G3A 0.491935 0.802326
99 BIS 0.491667 0.833333
100 MAP 0.491379 0.8
101 COD 0.488722 0.895349
102 AP0 0.488372 0.823529
103 G5P 0.488 0.802326
104 7MD 0.488 0.926829
105 MYR AMP 0.487603 0.858824
106 ADP PO3 0.482143 0.8375
107 80F 0.481481 0.83908
108 OMR 0.48062 0.870588
109 TSB 0.478632 0.758242
110 A5A 0.478261 0.766667
111 GA7 0.47619 0.853659
112 AFH 0.47619 0.835294
113 25L 0.47541 0.829268
114 SSA 0.474138 0.78022
115 BT5 0.474074 0.872093
116 NAX 0.472868 0.869048
117 TXD 0.472868 0.855422
118 DQV 0.472441 0.851852
119 GTA 0.472441 0.795455
120 GJV 0.472222 0.77381
121 TYR AMP 0.472 0.865854
122 6RE 0.471698 0.761905
123 M24 0.471014 0.804598
124 LSS 0.470588 0.763441
125 54H 0.470085 0.75
126 VMS 0.470085 0.75
127 TXE 0.469231 0.855422
128 SA8 0.469027 0.795181
129 JB6 0.467213 0.833333
130 5CA 0.466102 0.78022
131 53H 0.466102 0.741935
132 ADP ALF 0.465517 0.77907
133 ALF ADP 0.465517 0.77907
134 5X8 0.464286 0.765432
135 5AS 0.463636 0.76087
136 J7C 0.462963 0.771084
137 K15 0.46281 0.788235
138 LMS 0.462264 0.744444
139 DND 0.461538 0.853659
140 VO4 ADP 0.461538 0.829268
141 6V0 0.461538 0.845238
142 S7M 0.461538 0.755814
143 SMM 0.461538 0.75
144 ADP VO4 0.461538 0.829268
145 NXX 0.461538 0.853659
146 GSU 0.459016 0.8
147 DSZ 0.458333 0.78022
148 52H 0.457627 0.741935
149 EEM 0.456897 0.755814
150 62X 0.454545 0.770115
151 NVA LMS 0.454545 0.774194
152 7MC 0.454545 0.927711
153 YSA 0.452381 0.76087
154 G5A 0.452174 0.8
155 SAI 0.452174 0.780488
156 CNA 0.451852 0.853659
157 SFG 0.451327 0.797468
158 LEU LMS 0.45082 0.755319
159 TAD 0.449612 0.835294
160 AMP DBH 0.448819 0.797619
161 A A 0.447154 0.817073
162 0UM 0.446281 0.829268
163 FB0 0.445946 0.865169
164 BTX 0.445255 0.860465
165 T5A 0.444444 0.860465
166 ADJ 0.444444 0.870588
167 NAQ 0.443662 0.823529
168 LPA AMP 0.442748 0.837209
169 AOC 0.440367 0.753086
170 SAH 0.439655 0.790123
171 UP5 0.439394 0.843373
172 ADP BMA 0.439024 0.841463
173 A3D 0.438849 0.864198
174 KH3 0.438462 0.8
175 NAE 0.43662 0.843373
176 AF3 ADP 3PG 0.43609 0.813953
177 SAM 0.435897 0.755814
178 5N5 0.435644 0.75
179 AHZ 0.435115 0.816092
180 NAD 0.434783 0.851852
181 2A5 0.434783 0.841463
182 EAD 0.434483 0.847059
183 NSS 0.434426 0.76087
184 ATP A A A 0.433071 0.82716
185 4TC 0.432836 0.845238
186 UPA 0.432836 0.855422
187 EP4 0.432692 0.714286
188 PPS 0.432203 0.744444
189 5CD 0.431373 0.716049
190 PAP 0.431034 0.82716
191 XYA 0.43 0.75
192 ADN 0.43 0.75
193 RAB 0.43 0.75
194 3DH 0.429907 0.710843
195 8X1 0.429752 0.793478
196 A4P 0.42963 0.820225
197 0WD 0.42446 0.823529
198 P5A 0.424 0.824176
199 6IA 0.423729 0.857143
200 139 0.423358 0.869048
201 P1H 0.422819 0.848837
202 NDE 0.422819 0.831325
203 8PZ 0.421875 0.76087
204 COO 0.421053 0.886364
205 A3S 0.421053 0.7875
206 ZID 0.42069 0.841463
207 9K8 0.420635 0.701031
208 7D5 0.420561 0.804878
209 6AD 0.420168 0.793103
210 AR6 AR6 0.419847 0.839506
211 7D3 0.419643 0.807229
212 ARU 0.419355 0.772727
213 ATR 0.418803 0.814815
214 A4D 0.417476 0.728395
215 ITT 0.417391 0.792683
216 7D4 0.417391 0.807229
217 MHZ 0.417391 0.781609
218 A3P 0.415929 0.8375
219 NAJ PZO 0.415493 0.802326
220 DTA 0.415094 0.722892
221 M2T 0.415094 0.678161
222 WSA 0.414815 0.769231
223 A3T 0.413793 0.775
224 NAJ PYZ 0.413793 0.766667
225 ETB 0.412587 0.852273
226 F0P 0.411765 0.817073
227 DZD 0.411348 0.857143
228 MTA 0.411215 0.710843
229 A3N 0.410714 0.743902
230 A2R 0.409836 0.851852
231 P5F 0.408537 0.822222
232 AMX 0.408163 0.895349
233 S4M 0.40708 0.75
234 KB1 0.40625 0.764706
235 CMX 0.405405 0.906977
236 A G 0.404255 0.790698
237 AMP NAD 0.404255 0.851852
238 G A A A 0.404255 0.802326
239 CA6 0.403974 0.785714
240 MAO 0.403509 0.802326
241 A2P 0.403509 0.825
242 VRT 0.403361 0.792683
243 GEK 0.403226 0.783133
244 NDP 0.402878 0.823529
245 DCA 0.402778 0.863636
246 CO7 0.402597 0.886364
247 NEC 0.401786 0.728395
248 A3G 0.401786 0.8
249 3NZ 0.401575 0.783133
250 U A G G 0.401408 0.790698
251 NMX 0.401316 0.819149
252 HAX 0.4 0.865169
253 3AM 0.4 0.825
254 V3L 0.4 0.8625
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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