Receptor
PDB id Resolution Class Description Source Keywords
2Q7H 2.1 Å EC: 6.1.1.26 PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED PYRROLYSINE A PYROPHOSPHATE METHANOSARCINA MAZEI PYRROLYSYL-TRNA SYNTHETASE PYRROLYSINE LIGASE
Ref.: STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE, AN ARCHAEA FOR GENETIC CODE INNOVATION. PROC.NATL.ACAD.SCI.USA V. 104 11268 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:902;
A:903;
A:904;
A:905;
A:906;
A:907;
A:908;
A:909;
A:910;
A:911;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
POP A:901;
Invalid;
none;
submit data
175.959 H2 O7 P2 O[P@@...
YLY A:900;
Valid;
none;
submit data
586.535 C22 H35 N8 O9 P C[C@@...
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: YLY; Similar ligands found: 197
No: Ligand ECFP6 Tc MDL keys Tc
1 YLY 1 1
2 YLP 0.754386 0.963855
3 YLB 0.735043 0.963855
4 YLC 0.720339 0.939759
5 AYB 0.710744 0.952381
6 YLA 0.702479 0.917647
7 LAD 0.6875 0.939024
8 N0B 0.656489 0.917647
9 SRP 0.625 0.890244
10 ME8 0.623932 0.894118
11 5AL 0.607143 0.865854
12 AMO 0.603448 0.86747
13 NB8 0.596639 0.837209
14 YAP 0.595041 0.857143
15 8LH 0.582609 0.890244
16 FA5 0.581967 0.86747
17 8QN 0.581197 0.865854
18 CA0 0.567568 0.833333
19 4AD 0.563025 0.857143
20 PAJ 0.563025 0.848837
21 PTJ 0.557377 0.837209
22 8LE 0.551724 0.835294
23 PR8 0.54918 0.951219
24 KG4 0.548673 0.833333
25 8LQ 0.546219 0.890244
26 TYM 0.541985 0.86747
27 XAH 0.539683 0.894118
28 TXA 0.532258 0.845238
29 AT4 0.530973 0.781609
30 F2R 0.529412 0.873563
31 M33 0.526316 0.821429
32 A1R 0.52459 0.891566
33 WAQ 0.524194 0.914634
34 A2D 0.522523 0.809524
35 AHX 0.520325 0.837209
36 DLL 0.520325 0.843373
37 1ZZ 0.52 0.939759
38 AN2 0.517544 0.8
39 PRX 0.517241 0.855422
40 ANP 0.516949 0.790698
41 3UK 0.516129 0.833333
42 BA3 0.513274 0.809524
43 45A 0.508929 0.831325
44 ABM 0.508929 0.831325
45 AP5 0.508772 0.809524
46 B4P 0.508772 0.809524
47 ADP 0.508772 0.809524
48 3OD 0.507937 0.855422
49 IOT 0.507353 0.906977
50 AR6 0.504274 0.831325
51 APR 0.504274 0.831325
52 OOB 0.504065 0.843373
53 AU1 0.5 0.790698
54 A3R 0.5 0.891566
55 B5V 0.5 0.823529
56 ADX 0.5 0.73913
57 9SN 0.5 0.795455
58 LAQ 0.496241 0.850575
59 B5Y 0.496124 0.835294
60 00A 0.496 0.804598
61 ACP 0.495726 0.811765
62 50T 0.495726 0.77907
63 HEJ 0.495726 0.809524
64 ATP 0.495726 0.809524
65 A 0.495495 0.807229
66 AMP 0.495495 0.807229
67 ARG AMP 0.492424 0.862069
68 5SV 0.491935 0.903614
69 9ZA 0.491935 0.825581
70 9ZD 0.491935 0.825581
71 AQP 0.491525 0.809524
72 5FA 0.491525 0.809524
73 AD9 0.487395 0.790698
74 SAP 0.487395 0.772727
75 AGS 0.487395 0.772727
76 B5M 0.484615 0.835294
77 FYA 0.484375 0.843373
78 DAL AMP 0.483871 0.843373
79 4UU 0.481203 0.813953
80 OAD 0.480315 0.855422
81 ACQ 0.479339 0.811765
82 BT5 0.478873 0.863636
83 4UW 0.477941 0.827586
84 NAI 0.477941 0.784091
85 ADQ 0.47619 0.833333
86 A12 0.474138 0.823529
87 AP2 0.474138 0.823529
88 8X1 0.472 0.768421
89 COD 0.471831 0.908046
90 ATF 0.471545 0.781609
91 AFH 0.470149 0.806818
92 7MD 0.470149 0.916667
93 9X8 0.46875 0.813953
94 OZV 0.468254 0.809524
95 6YZ 0.467742 0.811765
96 TAT 0.467213 0.781609
97 GAP 0.467213 0.855422
98 T99 0.467213 0.781609
99 NAX 0.467153 0.818182
100 4UV 0.466165 0.813953
101 SON 0.466102 0.86747
102 SRA 0.464912 0.770115
103 HQG 0.464 0.821429
104 OMR 0.463768 0.928571
105 ADV 0.46281 0.845238
106 RBY 0.46281 0.845238
107 G3A 0.462687 0.775281
108 BIS 0.461538 0.804598
109 A22 0.460317 0.8
110 MAP 0.460317 0.772727
111 G5P 0.459259 0.775281
112 MYR AMP 0.458015 0.916667
113 25A 0.456693 0.809524
114 GTA 0.455882 0.769231
115 APC 0.454545 0.823529
116 P5A 0.453846 0.817204
117 KAA 0.453846 0.806452
118 ADP MG 0.453782 0.807229
119 TXE 0.453237 0.825581
120 AP0 0.45 0.795455
121 48N 0.449275 0.858824
122 53H 0.448819 0.71875
123 GA7 0.448529 0.845238
124 TXD 0.446043 0.825581
125 DQV 0.445255 0.821429
126 TYR AMP 0.444444 0.835294
127 BTX 0.441379 0.852273
128 VMS 0.440945 0.726316
129 54H 0.440945 0.726316
130 7MC 0.439716 0.940476
131 JB6 0.439394 0.825581
132 ATP MG 0.439024 0.807229
133 ADP PO3 0.439024 0.807229
134 APC MG 0.439024 0.809524
135 LPA AMP 0.438849 0.829545
136 CNA 0.4375 0.823529
137 TSB 0.4375 0.734043
138 A5A 0.436508 0.741935
139 M24 0.436242 0.777778
140 25L 0.43609 0.8
141 NXX 0.435714 0.823529
142 DND 0.435714 0.823529
143 6V0 0.435714 0.795455
144 80F 0.435374 0.791209
145 FB0 0.433121 0.920455
146 SSA 0.433071 0.755319
147 J7C 0.432203 0.744186
148 GSU 0.431818 0.774194
149 DSZ 0.430769 0.755319
150 LSS 0.430769 0.757895
151 ADJ 0.430556 0.840909
152 T5A 0.430556 0.831461
153 GJV 0.428571 0.747126
154 6RE 0.42735 0.735632
155 A4P 0.426573 0.774194
156 5CA 0.426357 0.755319
157 UP5 0.425532 0.793103
158 ALF ADP 0.425197 0.752809
159 ADP ALF 0.425197 0.752809
160 G5A 0.424 0.774194
161 SMM 0.421875 0.784091
162 ADP VO4 0.421875 0.8
163 VO4 ADP 0.421875 0.8
164 NAD 0.421769 0.821429
165 5AS 0.421488 0.755319
166 J4G 0.421053 0.879518
167 139 0.42069 0.83908
168 UPA 0.41958 0.804598
169 4TC 0.41958 0.795455
170 LMS 0.418803 0.72043
171 52H 0.418605 0.71875
172 NVA LMS 0.416667 0.768421
173 A3D 0.416107 0.833333
174 YSA 0.416058 0.736842
175 SA8 0.416 0.809524
176 TAD 0.414286 0.806818
177 K15 0.413534 0.845238
178 AMP DBH 0.413043 0.770115
179 AF3 ADP 3PG 0.412587 0.786517
180 AOC 0.411765 0.705882
181 NAQ 0.411765 0.816092
182 NDC 0.40625 0.858824
183 EEM 0.40625 0.770115
184 62X 0.406015 0.825581
185 NAE 0.405229 0.835294
186 EAD 0.403846 0.797753
187 ADP BMA 0.402985 0.811765
188 LEU LMS 0.402985 0.75
189 0WD 0.402685 0.775281
190 SAI 0.401575 0.752941
191 AHZ 0.401408 0.829545
192 ETB 0.401316 0.886364
193 5X8 0.4 0.738095
194 S7M 0.4 0.770115
195 DZD 0.4 0.848837
196 SFG 0.4 0.768293
197 A A 0.4 0.788235
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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