Receptor
PDB id Resolution Class Description Source Keywords
2ZIO 2.06 Å EC: 6.1.1.26 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PYRROLYSYL- TRNA SYNTHETASE IN COMPLEX WITH ALOCLYS-AMP AND PNP METHANOSARCINA MAZEI AMINOACYL-TRNA SYNTHETASE PYRROLYSYL-TRNA SYNTHETASE TRNAPYRROLYSINE ATP ANALOGUE NON-NATURAL AMINO ACID UNNATURAL AMINO ACID ATP-BINDING CYTOPLASM LIGASE NUCLEOTIDE-BINDING PROTEIN BIOSYNTHESIS STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: MULTISTEP ENGINEERING OF PYRROLYSYL-TRNA SYNTHETASE TO GENETICALLY ENCODE N(VAREPSILON)-(O-AZIDOBENZYLOXYCARBONYL) LYSINE FOR SITE-SPECIFIC PROTEIN MODIFICATION CHEM.BIOL. V. 15 1187 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2PN A:1;
Valid;
none;
submit data
176.99 H5 N O6 P2 N(P(=...
AYB A:601;
Valid;
none;
submit data
561.483 C20 H32 N7 O10 P CCCOC...
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: 2PN; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 2PN 1 1
2 PPK 0.473684 0.9
Ligand no: 2; Ligand: AYB; Similar ligands found: 235
No: Ligand ECFP6 Tc MDL keys Tc
1 AYB 1 1
2 YLA 0.825688 0.940476
3 YLP 0.803738 0.963855
4 YLB 0.798165 0.987805
5 YLC 0.765766 0.939759
6 N0B 0.75 0.940476
7 LAD 0.75 0.939024
8 YLY 0.710744 0.952381
9 SRP 0.666667 0.890244
10 ME8 0.663636 0.872093
11 5AL 0.647619 0.865854
12 AMO 0.642202 0.86747
13 NB8 0.633929 0.837209
14 8QN 0.618182 0.865854
15 4AD 0.612613 0.857143
16 PRX 0.609524 0.878049
17 CA0 0.605769 0.855422
18 FA5 0.603448 0.86747
19 YAP 0.603448 0.857143
20 PAJ 0.598214 0.848837
21 XAH 0.584746 0.894118
22 PTJ 0.577586 0.837209
23 TYM 0.572581 0.86747
24 F2R 0.570312 0.873563
25 TXA 0.564103 0.86747
26 1ZZ 0.564103 0.916667
27 5SV 0.561404 0.880952
28 M33 0.560748 0.821429
29 A2D 0.557692 0.809524
30 WAQ 0.555556 0.914634
31 DLL 0.551724 0.843373
32 AHX 0.551724 0.837209
33 AN2 0.551402 0.8
34 BA3 0.54717 0.809524
35 IOT 0.546875 0.906977
36 ABM 0.542857 0.809524
37 AP5 0.542056 0.809524
38 ADP 0.542056 0.809524
39 B4P 0.542056 0.809524
40 AT4 0.537037 0.781609
41 AR6 0.536364 0.831325
42 APR 0.536364 0.831325
43 ANP 0.535714 0.790698
44 OOB 0.534483 0.843373
45 3UK 0.533898 0.833333
46 ARG AMP 0.532258 0.862069
47 ADX 0.53211 0.73913
48 B5V 0.529412 0.823529
49 9SN 0.528926 0.795455
50 AMP 0.528846 0.807229
51 A 0.528846 0.807229
52 ACP 0.527273 0.811765
53 ATP 0.527273 0.809524
54 HEJ 0.527273 0.809524
55 50T 0.527273 0.77907
56 DAL AMP 0.525862 0.843373
57 00A 0.525424 0.804598
58 B5Y 0.52459 0.835294
59 5FA 0.522523 0.809524
60 AQP 0.522523 0.809524
61 9ZA 0.521368 0.825581
62 9ZD 0.521368 0.825581
63 AU1 0.518182 0.790698
64 AD9 0.517857 0.790698
65 AGS 0.517857 0.772727
66 SAP 0.517857 0.772727
67 A1R 0.516949 0.891566
68 PR8 0.516667 0.951219
69 3OD 0.512397 0.855422
70 FYA 0.512397 0.843373
71 B5M 0.512195 0.835294
72 ACQ 0.508772 0.811765
73 OAD 0.508333 0.855422
74 A12 0.504587 0.823529
75 AP2 0.504587 0.823529
76 ATF 0.5 0.781609
77 7MD 0.496063 0.916667
78 4UU 0.496063 0.813953
79 MYR AMP 0.495935 0.894118
80 9X8 0.495868 0.813953
81 6YZ 0.495726 0.811765
82 T99 0.495652 0.781609
83 GAP 0.495652 0.855422
84 TAT 0.495652 0.781609
85 SON 0.495495 0.86747
86 SRA 0.495327 0.770115
87 4UW 0.492308 0.806818
88 NAI 0.492308 0.784091
89 4UV 0.492063 0.813953
90 KAA 0.491803 0.806452
91 ADV 0.491228 0.845238
92 RBY 0.491228 0.845238
93 OMR 0.48855 0.905882
94 LAQ 0.488372 0.850575
95 BIS 0.487805 0.804598
96 A22 0.487395 0.8
97 25A 0.483333 0.809524
98 APC 0.482456 0.823529
99 DQV 0.48062 0.821429
100 A3R 0.479339 0.891566
101 ADQ 0.479339 0.833333
102 80F 0.478261 0.791209
103 G3A 0.476562 0.775281
104 JB6 0.475806 0.825581
105 MAP 0.475 0.772727
106 COD 0.474453 0.908046
107 AP0 0.473684 0.775281
108 7MC 0.473684 0.917647
109 48N 0.473282 0.837209
110 G5P 0.472868 0.775281
111 BT5 0.471014 0.863636
112 TXD 0.469697 0.825581
113 NAX 0.469697 0.818182
114 TYR AMP 0.46875 0.835294
115 TXE 0.466165 0.825581
116 ADP PO3 0.465517 0.807229
117 NVA LMS 0.463415 0.787234
118 53H 0.46281 0.71875
119 TSB 0.46281 0.734043
120 A5A 0.462185 0.741935
121 AFH 0.461538 0.806818
122 GA7 0.461538 0.845238
123 25L 0.460317 0.8
124 5AS 0.460177 0.774194
125 K15 0.459677 0.823529
126 J7C 0.459459 0.744186
127 SSA 0.458333 0.755319
128 GTA 0.458015 0.769231
129 M24 0.457746 0.777778
130 GJV 0.455357 0.747126
131 LSS 0.455285 0.757895
132 54H 0.454545 0.726316
133 VMS 0.454545 0.726316
134 6RE 0.454545 0.735632
135 5CA 0.45082 0.755319
136 ALF ADP 0.45 0.752809
137 ADP ALF 0.45 0.752809
138 UP5 0.447761 0.793103
139 DND 0.447761 0.823529
140 NXX 0.447761 0.823529
141 6V0 0.447761 0.795455
142 ADP VO4 0.446281 0.8
143 SMM 0.446281 0.744444
144 VO4 ADP 0.446281 0.8
145 LMS 0.445455 0.72043
146 GSU 0.444444 0.774194
147 FB0 0.443709 0.877778
148 0UM 0.443548 0.865854
149 DSZ 0.443548 0.755319
150 BTX 0.442857 0.852273
151 52H 0.442623 0.71875
152 ADJ 0.442029 0.840909
153 NAQ 0.441379 0.816092
154 4TC 0.441176 0.795455
155 9K8 0.440945 0.69697
156 SA8 0.440678 0.788235
157 CNA 0.438849 0.823529
158 G5A 0.436975 0.774194
159 LEU LMS 0.436508 0.75
160 KH3 0.43609 0.835294
161 TAD 0.43609 0.806818
162 AMP DBH 0.435115 0.770115
163 NAE 0.434483 0.835294
164 S7M 0.434426 0.75
165 AHZ 0.432836 0.788889
166 EAD 0.432432 0.818182
167 NSS 0.432 0.736842
168 T5A 0.431655 0.831461
169 UPA 0.430657 0.804598
170 P1H 0.430464 0.840909
171 EEM 0.429752 0.75
172 LPA AMP 0.42963 0.829545
173 62X 0.428571 0.784091
174 ARU 0.428571 0.766667
175 A4P 0.427536 0.774194
176 YSA 0.427481 0.736842
177 3DH 0.427273 0.705882
178 A3D 0.426573 0.833333
179 ADP BMA 0.425197 0.811765
180 SAI 0.425 0.752941
181 AOC 0.424779 0.705882
182 SFG 0.423729 0.768293
183 5X8 0.423729 0.738095
184 NAJ PZO 0.423611 0.755556
185 AF3 ADP 3PG 0.423358 0.786517
186 NAD 0.422535 0.821429
187 A A 0.421875 0.788235
188 6IA 0.421488 0.848837
189 SAM 0.421488 0.75
190 139 0.421429 0.83908
191 2A5 0.420168 0.833333
192 EP4 0.416667 0.709302
193 PAP 0.416667 0.797619
194 8X1 0.416 0.768421
195 5CD 0.415094 0.690476
196 ADN 0.413462 0.722892
197 RAB 0.413462 0.722892
198 XYA 0.413462 0.722892
199 SAH 0.413223 0.761905
200 WSA 0.413043 0.744681
201 0WD 0.412587 0.775281
202 NAJ PYZ 0.412162 0.723404
203 P5A 0.410853 0.817204
204 ZID 0.409396 0.811765
205 ATP A A A 0.409091 0.797619
206 MTA 0.409091 0.705882
207 8PZ 0.409091 0.736842
208 A2R 0.408 0.821429
209 A3S 0.40678 0.759036
210 PPS 0.406504 0.72043
211 6AD 0.406504 0.766667
212 CAJ 0.406452 0.920455
213 5N5 0.40566 0.722892
214 0T1 0.405405 0.91954
215 7D5 0.405405 0.776471
216 S4M 0.405172 0.764045
217 7D3 0.405172 0.77907
218 ATR 0.404959 0.785714
219 7D4 0.403361 0.77907
220 MHZ 0.403361 0.795455
221 AMP NAD 0.402778 0.821429
222 NDE 0.402597 0.802326
223 A4D 0.401869 0.702381
224 MAO 0.401709 0.795455
225 A3P 0.401709 0.807229
226 VRT 0.401639 0.807229
227 GEK 0.401575 0.755814
228 ETB 0.401361 0.844444
229 DCA 0.401361 0.897727
230 BVT 0.40107 0.860215
231 DZD 0.4 0.848837
232 NEC 0.4 0.722892
233 A3T 0.4 0.746988
234 M2T 0.4 0.674157
235 DTA 0.4 0.697674
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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