Receptor
PDB id Resolution Class Description Source Keywords
4BWA 2.45 Å EC: 6.1.1.26 PYLRS Y306G, Y384F, I405R MUTANT IN COMPLEX WITH ADENYLATED NORBORNENE METHANOSARCINA MAZEI LIGASE
Ref.: STRUCTURAL INSIGHTS INTO INCORPORATION OF NORBORNEN ACIDS FOR CLICK MODIFICATION OF PROTEINS CHEM.BIO.CHEM. V. 14 2114 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEG A:1457;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
EDO A:1458;
A:1459;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
N0B A:1456;
Valid;
none;
submit data
625.568 C25 H36 N7 O10 P c1nc(...
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
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: N0B; Similar ligands found: 177
No: Ligand ECFP6 Tc MDL keys Tc
1 N0B 1 1
2 YLA 0.756303 0.97561
3 AYB 0.75 0.940476
4 YLP 0.705882 0.928571
5 YLB 0.702479 0.928571
6 YLC 0.688525 0.951219
7 LAD 0.684211 0.950617
8 YLY 0.656489 0.917647
9 SRP 0.608696 0.901235
10 ME8 0.595041 0.83908
11 AMO 0.588235 0.878049
12 NB8 0.581967 0.847059
13 5AL 0.577586 0.853659
14 4AD 0.575 0.86747
15 YAP 0.555556 0.890244
16 FA5 0.555556 0.901235
17 8LH 0.554622 0.855422
18 8QN 0.553719 0.853659
19 CA0 0.552632 0.865854
20 XAH 0.551181 0.904762
21 PAJ 0.54918 0.816092
22 KG4 0.534483 0.843373
23 8LQ 0.532787 0.855422
24 PTJ 0.531746 0.804598
25 TYM 0.529851 0.901235
26 F2R 0.528986 0.883721
27 AHX 0.52 0.847059
28 DLL 0.52 0.876543
29 BA3 0.513043 0.841463
30 8LE 0.512397 0.823529
31 A2D 0.508772 0.841463
32 AP5 0.508621 0.841463
33 B4P 0.508621 0.841463
34 TXA 0.507812 0.855422
35 AN2 0.504274 0.809524
36 OOB 0.504 0.876543
37 3UK 0.503937 0.865854
38 ARG AMP 0.503759 0.872093
39 B5V 0.5 0.855422
40 WAQ 0.5 0.925926
41 M33 0.5 0.809524
42 IOT 0.496403 0.917647
43 ATP 0.495798 0.819277
44 50T 0.495798 0.788235
45 HEJ 0.495798 0.819277
46 ADP 0.495726 0.819277
47 ANP 0.491803 0.8
48 5FA 0.491667 0.819277
49 PRX 0.491667 0.821429
50 AQP 0.491667 0.819277
51 AT4 0.491525 0.790698
52 9SN 0.48855 0.825581
53 PR8 0.488372 0.962963
54 A1R 0.488189 0.902439
55 AGS 0.487603 0.781609
56 SAP 0.487603 0.781609
57 ADX 0.487395 0.747253
58 1ZZ 0.484615 0.860465
59 00A 0.484375 0.835294
60 DAL AMP 0.484127 0.831325
61 ACP 0.483333 0.821429
62 45A 0.482759 0.797619
63 ABM 0.482759 0.797619
64 A 0.482456 0.817073
65 AMP 0.482456 0.817073
66 5SV 0.480315 0.825581
67 AR6 0.479339 0.841463
68 APR 0.479339 0.841463
69 AD9 0.47541 0.8
70 AU1 0.475 0.8
71 B5Y 0.473684 0.845238
72 B5M 0.473684 0.845238
73 FYA 0.473282 0.876543
74 3OD 0.473282 0.843373
75 4UU 0.470588 0.86747
76 OZV 0.46875 0.819277
77 9ZA 0.46875 0.813953
78 9ZD 0.46875 0.813953
79 6YZ 0.468254 0.821429
80 ACQ 0.467742 0.821429
81 GAP 0.467742 0.865854
82 NAI 0.467626 0.835294
83 4UV 0.466667 0.86747
84 A3R 0.465116 0.902439
85 LAQ 0.463768 0.860465
86 AP2 0.462185 0.833333
87 A12 0.462185 0.833333
88 ATF 0.460317 0.790698
89 7MD 0.459854 0.927711
90 OAD 0.458015 0.843373
91 4UW 0.457143 0.837209
92 TAT 0.456 0.790698
93 T99 0.456 0.790698
94 SON 0.454545 0.878049
95 KAA 0.454545 0.815217
96 HQG 0.453125 0.831325
97 SRA 0.452991 0.77907
98 G3A 0.452555 0.804598
99 BIS 0.451128 0.813953
100 A22 0.449612 0.831325
101 G5P 0.449275 0.804598
102 BT5 0.44898 0.873563
103 9X8 0.44697 0.802326
104 TXD 0.446809 0.879518
105 25A 0.446154 0.841463
106 80F 0.445946 0.840909
107 TYR AMP 0.445255 0.86747
108 TXE 0.443662 0.879518
109 APC 0.443548 0.833333
110 ADQ 0.442748 0.865854
111 ADP MG 0.442623 0.817073
112 AP0 0.440559 0.804598
113 RBY 0.44 0.855422
114 APC MG 0.44 0.819277
115 ADV 0.44 0.855422
116 GA7 0.438849 0.833333
117 AFH 0.438849 0.837209
118 MAP 0.438462 0.781609
119 25L 0.437037 0.831325
120 NAX 0.43662 0.870588
121 NXX 0.43662 0.855422
122 DND 0.43662 0.855422
123 6V0 0.43662 0.847059
124 DQV 0.435714 0.853659
125 GTA 0.435714 0.777778
126 SSA 0.434109 0.763441
127 COD 0.432432 0.875
128 BTX 0.432432 0.862069
129 T5A 0.431507 0.862069
130 48N 0.429577 0.825581
131 ADP PO3 0.428571 0.817073
132 ATP MG 0.428571 0.817073
133 CNA 0.428571 0.855422
134 M24 0.427632 0.806818
135 A4P 0.427586 0.822222
136 MYR AMP 0.426471 0.83908
137 OMR 0.423611 0.850575
138 ADP VO4 0.423077 0.809524
139 VO4 ADP 0.423077 0.809524
140 NAD 0.422819 0.853659
141 ADJ 0.421769 0.894118
142 LSS 0.421053 0.729167
143 DSZ 0.421053 0.763441
144 7MC 0.42069 0.905882
145 54H 0.419847 0.715789
146 VMS 0.419847 0.715789
147 JB6 0.419118 0.857143
148 GJV 0.418033 0.755814
149 NVA LMS 0.41791 0.739583
150 TSB 0.416667 0.723404
151 6RE 0.416667 0.744186
152 5CA 0.416667 0.763441
153 53H 0.416667 0.708333
154 FB0 0.416149 0.846154
155 A5A 0.415385 0.731183
156 ADP ALF 0.415385 0.761364
157 ALF ADP 0.415385 0.761364
158 G5A 0.414062 0.782609
159 139 0.412162 0.892857
160 J4G 0.411765 0.890244
161 GSU 0.411765 0.782609
162 NSS 0.410448 0.744681
163 J7C 0.409836 0.752941
164 LPA AMP 0.409722 0.83908
165 LMS 0.408333 0.728261
166 A3D 0.407895 0.843373
167 UP5 0.406897 0.845238
168 TAD 0.405594 0.816092
169 LEU LMS 0.404412 0.721649
170 K15 0.404412 0.770115
171 AMP DBH 0.404255 0.8
172 NAQ 0.403846 0.804598
173 5X8 0.401575 0.746988
174 SFG 0.401575 0.777778
175 SMM 0.401515 0.714286
176 DZD 0.401316 0.880952
177 5AS 0.4 0.744681
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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