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 (40)
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 6LY6 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
4 6LYB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 6LY7 - TRF C12 H12 N2 O3 c1ccc2c(c1....
7 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
8 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
9 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
10 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
11 6AAQ Kd = 3.9 mM 9U9 C17 H26 N2 O4 C1C[C@@H]2....
12 6AAO Kd = 7.8 mM 9U0 C15 H26 N2 O4 C1CCC=CC(C....
13 6AAP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
14 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
15 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
16 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
17 6AB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
19 6ABM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4CS3 - AMP LYS FU0 n/a n/a
22 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
23 6AAN Kd = 1.76 mM 9TX C16 H20 N2 O4 C#Cc1cccc(....
24 6LY3 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
26 6AB1 - 9V0 C14 H19 N5 O4 c1ccc(c(c1....
27 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
28 6ABK Kd = 11.3 mM 9VF C11 H24 N2 O4 Si C[Si](C)(C....
29 6AAC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
31 6AB0 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
32 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
33 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
34 6AAD Kd = 1.62 mM 9TU C16 H19 F3 N4 O4 c1cc(cc(c1....
35 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
36 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
37 2ZCE - PYL C12 H21 N3 O3 C[C@@H]1CC....
38 6AAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
39 6AB8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
40 6LYA - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
70% Homology Family (40)
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 6LY6 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
4 6LYB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 6LY7 - TRF C12 H12 N2 O3 c1ccc2c(c1....
7 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
8 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
9 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
10 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
11 6AAQ Kd = 3.9 mM 9U9 C17 H26 N2 O4 C1C[C@@H]2....
12 6AAO Kd = 7.8 mM 9U0 C15 H26 N2 O4 C1CCC=CC(C....
13 6AAP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
14 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
15 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
16 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
17 6AB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
19 6ABM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4CS3 - AMP LYS FU0 n/a n/a
22 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
23 6AAN Kd = 1.76 mM 9TX C16 H20 N2 O4 C#Cc1cccc(....
24 6LY3 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
26 6AB1 - 9V0 C14 H19 N5 O4 c1ccc(c(c1....
27 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
28 6ABK Kd = 11.3 mM 9VF C11 H24 N2 O4 Si C[Si](C)(C....
29 6AAC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
31 6AB0 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
32 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
33 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
34 6AAD Kd = 1.62 mM 9TU C16 H19 F3 N4 O4 c1cc(cc(c1....
35 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
36 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
37 2ZCE - PYL C12 H21 N3 O3 C[C@@H]1CC....
38 6AAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
39 6AB8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
40 6LYA - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
50% Homology Family (40)
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 6LY6 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 2ZIN - LBY C11 H22 N2 O4 CC(C)(C)OC....
4 6LYB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 5K1P - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 6LY7 - TRF C12 H12 N2 O3 c1ccc2c(c1....
7 4CH4 - YLC C20 H30 N7 O9 P C/C=C/C(=O....
8 4BW9 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
9 5K1X - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
10 4CS4 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
11 6AAQ Kd = 3.9 mM 9U9 C17 H26 N2 O4 C1C[C@@H]2....
12 6AAO Kd = 7.8 mM 9U0 C15 H26 N2 O4 C1CCC=CC(C....
13 6AAP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
14 4BWA - N0B C25 H36 N7 O10 P c1nc(c2c(n....
15 4TQD - 33S C9 H10 I N O2 c1cc(cc(c1....
16 4ZIB - 4OG C11 H11 N O2 S c1ccc2c(c1....
17 6AB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 4CH5 - YLP C19 H30 N7 O9 P CCC(=O)NCC....
19 6ABM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 3QTC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4CS3 - AMP LYS FU0 n/a n/a
22 2ZIO - AYB C20 H32 N7 O10 P CCCOC(=O)N....
23 6AAN Kd = 1.76 mM 9TX C16 H20 N2 O4 C#Cc1cccc(....
24 6LY3 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 2Q7G - CCL C12 H22 N2 O4 C1CCC(C1)O....
26 6AB1 - 9V0 C14 H19 N5 O4 c1ccc(c(c1....
27 2Q7E - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
28 6ABK Kd = 11.3 mM 9VF C11 H24 N2 O4 Si C[Si](C)(C....
29 6AAC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 2Q7H - YLY C22 H35 N8 O9 P C[C@@H]1CC....
31 6AB0 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
32 4Q6G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
33 4CH3 - YLB C20 H32 N7 O9 P CCCC(=O)NC....
34 6AAD Kd = 1.62 mM 9TU C16 H19 F3 N4 O4 c1cc(cc(c1....
35 2ZIM - YLY C22 H35 N8 O9 P C[C@@H]1CC....
36 4CH6 - YLA C20 H28 N7 O10 P C#CCOC(=O)....
37 2ZCE - PYL C12 H21 N3 O3 C[C@@H]1CC....
38 6AAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
39 6AB8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
40 6LYA - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: N0B; Similar ligands found: 186
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 FA5 0.555556 0.901235
16 8LH 0.554622 0.855422
17 8QN 0.553719 0.853659
18 CA0 0.552632 0.865854
19 XAH 0.551181 0.904762
20 PAJ 0.54918 0.816092
21 KG4 0.534483 0.843373
22 QA7 0.532787 0.823529
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 M33 0.5 0.809524
40 WAQ 0.5 0.925926
41 B5V 0.5 0.855422
42 IOT 0.496403 0.917647
43 50T 0.495798 0.788235
44 ATP 0.495798 0.819277
45 HEJ 0.495798 0.819277
46 ADP 0.495726 0.819277
47 ANP 0.491803 0.8
48 AQP 0.491667 0.819277
49 PRX 0.491667 0.821429
50 5FA 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 ADX 0.487395 0.747253
57 1ZZ 0.484615 0.860465
58 00A 0.484375 0.835294
59 DAL AMP 0.484127 0.831325
60 ACP 0.483333 0.821429
61 ABM 0.482759 0.797619
62 45A 0.482759 0.797619
63 A 0.482456 0.817073
64 AMP 0.482456 0.817073
65 5SV 0.480315 0.825581
66 AR6 0.479339 0.841463
67 APR 0.479339 0.841463
68 AD9 0.47541 0.8
69 AU1 0.475 0.8
70 B5M 0.473684 0.845238
71 B5Y 0.473684 0.845238
72 3OD 0.473282 0.843373
73 FYA 0.473282 0.876543
74 4UU 0.470588 0.86747
75 OZV 0.46875 0.819277
76 9ZA 0.46875 0.813953
77 9ZD 0.46875 0.813953
78 6YZ 0.468254 0.821429
79 ACQ 0.467742 0.821429
80 GAP 0.467742 0.865854
81 NAI 0.467626 0.835294
82 4UV 0.466667 0.86747
83 AMP MG 0.465517 0.804878
84 A3R 0.465116 0.902439
85 V2G 0.464 0.891566
86 LAQ 0.463768 0.860465
87 AP2 0.462185 0.833333
88 A12 0.462185 0.833333
89 JNT 0.461538 0.865854
90 ATF 0.460317 0.790698
91 7MD 0.459854 0.927711
92 OAD 0.458015 0.843373
93 4UW 0.457143 0.837209
94 T99 0.456 0.790698
95 TAT 0.456 0.790698
96 SON 0.454545 0.878049
97 KAA 0.454545 0.815217
98 HQG 0.453125 0.831325
99 SRA 0.452991 0.77907
100 G3A 0.452555 0.804598
101 BIS 0.451128 0.813953
102 A22 0.449612 0.831325
103 G5P 0.449275 0.804598
104 BT5 0.44898 0.873563
105 9X8 0.44697 0.802326
106 TXD 0.446809 0.879518
107 25A 0.446154 0.841463
108 80F 0.445946 0.840909
109 D4F 0.443709 0.818182
110 TXE 0.443662 0.879518
111 APC 0.443548 0.833333
112 ADQ 0.442748 0.865854
113 ADP BEF 0.442623 0.817073
114 ADP MG 0.442623 0.817073
115 AP0 0.440559 0.804598
116 RBY 0.44 0.855422
117 ADV 0.44 0.855422
118 APC MG 0.44 0.819277
119 AFH 0.438849 0.837209
120 GA7 0.438849 0.833333
121 MAP 0.438462 0.781609
122 ANP MG 0.4375 0.809524
123 25L 0.437037 0.831325
124 NAX 0.43662 0.870588
125 DND 0.43662 0.855422
126 6V0 0.43662 0.847059
127 DQV 0.435714 0.853659
128 GTA 0.435714 0.777778
129 SSA 0.434109 0.763441
130 COD 0.432432 0.875
131 BTX 0.432432 0.862069
132 T5A 0.431507 0.862069
133 KMQ 0.430657 0.833333
134 48N 0.429577 0.825581
135 ADP PO3 0.428571 0.817073
136 ATP MG 0.428571 0.817073
137 CNA 0.428571 0.855422
138 M24 0.427632 0.806818
139 A4P 0.427586 0.822222
140 KYE 0.427536 0.802326
141 MYR AMP 0.426471 0.83908
142 VO4 ADP 0.426357 0.8
143 BEF ADP 0.425197 0.797619
144 OMR 0.423611 0.850575
145 NAD 0.422819 0.853659
146 ADJ 0.421769 0.894118
147 DSZ 0.421053 0.763441
148 LSS 0.421053 0.729167
149 7MC 0.42069 0.905882
150 VMS 0.419847 0.715789
151 54H 0.419847 0.715789
152 JB6 0.419118 0.857143
153 GJV 0.418033 0.755814
154 NVA LMS 0.41791 0.739583
155 TSB 0.416667 0.723404
156 5CA 0.416667 0.763441
157 6RE 0.416667 0.744186
158 53H 0.416667 0.708333
159 FB0 0.416149 0.846154
160 KXW 0.415493 0.841463
161 A5A 0.415385 0.731183
162 ALF ADP 0.415385 0.761364
163 LEU LMS 0.414815 0.71875
164 G5A 0.414062 0.782609
165 139 0.412162 0.892857
166 GSU 0.411765 0.782609
167 J4G 0.411765 0.890244
168 L3W 0.410959 0.833333
169 NSS 0.410448 0.744681
170 J7C 0.409836 0.752941
171 LPA AMP 0.409722 0.83908
172 LMS 0.408333 0.728261
173 A3D 0.407895 0.843373
174 UP5 0.406897 0.845238
175 TAD 0.405594 0.816092
176 K15 0.404412 0.770115
177 AMP DBH 0.404255 0.8
178 ALF ADP 3PG 0.40411 0.795455
179 NAQ 0.403846 0.804598
180 SFG 0.401575 0.777778
181 5X8 0.401575 0.746988
182 SMM 0.401515 0.714286
183 NAD IBO 0.401361 0.841463
184 NAD TDB 0.401361 0.841463
185 DZD 0.401316 0.880952
186 5AS 0.4 0.744681
Similar Ligands (3D)
Ligand no: 1; Ligand: N0B; Similar ligands found: 0
No: Ligand Similarity coefficient
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: 16
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 3G1Z AMP 16.7883
6 3G1Z AMP 16.7883
7 3A5Y KAA 17.1533
8 3A5Y KAA 17.1533
9 3A5Z KAA 17.1533
10 3A5Z KAA 17.1533
11 3REU ATP 17.5182
12 3REU ATP 17.5182
13 3NEM ATP 18.2482
14 3NEM AMO 18.2482
15 3E9I XAH 22.2628
16 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: 16
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 3G1Z AMP 16.7883
6 3G1Z AMP 16.7883
7 3A5Y KAA 17.1533
8 3A5Y KAA 17.1533
9 3A5Z KAA 17.1533
10 3A5Z KAA 17.1533
11 3REU ATP 17.5182
12 3REU ATP 17.5182
13 3NEM ATP 18.2482
14 3NEM AMO 18.2482
15 3E9I XAH 22.2628
16 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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