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
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: N0B; Similar ligands found: 166
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 8QN 0.553719 0.853659
18 CA0 0.552632 0.865854
19 XAH 0.551181 0.904762
20 PAJ 0.54918 0.816092
21 PTJ 0.531746 0.804598
22 TYM 0.529851 0.901235
23 F2R 0.528986 0.883721
24 DLL 0.52 0.876543
25 AHX 0.52 0.847059
26 BA3 0.513043 0.841463
27 A2D 0.508772 0.841463
28 B4P 0.508621 0.841463
29 AP5 0.508621 0.841463
30 TXA 0.507812 0.855422
31 AN2 0.504274 0.809524
32 OOB 0.504 0.876543
33 3UK 0.503937 0.865854
34 ARG AMP 0.503759 0.872093
35 B5V 0.5 0.855422
36 M33 0.5 0.809524
37 WAQ 0.5 0.925926
38 IOT 0.496403 0.917647
39 ATP 0.495798 0.819277
40 50T 0.495798 0.788235
41 HEJ 0.495798 0.819277
42 ADP 0.495726 0.819277
43 ANP 0.491803 0.8
44 PRX 0.491667 0.821429
45 AQP 0.491667 0.819277
46 5FA 0.491667 0.819277
47 AT4 0.491525 0.790698
48 9SN 0.48855 0.825581
49 PR8 0.488372 0.962963
50 A1R 0.488189 0.902439
51 AGS 0.487603 0.781609
52 SAP 0.487603 0.781609
53 ADX 0.487395 0.747253
54 1ZZ 0.484615 0.860465
55 00A 0.484375 0.835294
56 DAL AMP 0.484127 0.831325
57 ACP 0.483333 0.821429
58 ABM 0.482759 0.797619
59 AMP 0.482456 0.817073
60 A 0.482456 0.817073
61 5SV 0.480315 0.825581
62 APR 0.479339 0.841463
63 AR6 0.479339 0.841463
64 AD9 0.47541 0.8
65 AU1 0.475 0.8
66 B5Y 0.473684 0.845238
67 B5M 0.473684 0.845238
68 3OD 0.473282 0.843373
69 FYA 0.473282 0.876543
70 4UU 0.470588 0.86747
71 9ZA 0.46875 0.813953
72 9ZD 0.46875 0.813953
73 6YZ 0.468254 0.821429
74 GAP 0.467742 0.865854
75 ACQ 0.467742 0.821429
76 NAI 0.467626 0.835294
77 4UV 0.466667 0.86747
78 A3R 0.465116 0.902439
79 LAQ 0.463768 0.860465
80 A12 0.462185 0.833333
81 AP2 0.462185 0.833333
82 ATF 0.460317 0.790698
83 7MD 0.459854 0.927711
84 OAD 0.458015 0.843373
85 4UW 0.457143 0.837209
86 T99 0.456 0.790698
87 TAT 0.456 0.790698
88 SON 0.454545 0.878049
89 KAA 0.454545 0.815217
90 SRA 0.452991 0.77907
91 G3A 0.452555 0.804598
92 BIS 0.451128 0.813953
93 A22 0.449612 0.831325
94 G5P 0.449275 0.804598
95 BT5 0.44898 0.873563
96 9X8 0.44697 0.802326
97 TXD 0.446809 0.879518
98 25A 0.446154 0.841463
99 80F 0.445946 0.840909
100 TYR AMP 0.445255 0.86747
101 TXE 0.443662 0.879518
102 APC 0.443548 0.833333
103 ADQ 0.442748 0.865854
104 AP0 0.440559 0.804598
105 RBY 0.44 0.855422
106 ADV 0.44 0.855422
107 GA7 0.438849 0.833333
108 AFH 0.438849 0.837209
109 MAP 0.438462 0.781609
110 25L 0.437037 0.831325
111 NXX 0.43662 0.855422
112 NAX 0.43662 0.870588
113 DND 0.43662 0.855422
114 6V0 0.43662 0.847059
115 GTA 0.435714 0.777778
116 DQV 0.435714 0.853659
117 SSA 0.434109 0.763441
118 COD 0.432432 0.875
119 BTX 0.432432 0.862069
120 T5A 0.431507 0.862069
121 48N 0.429577 0.825581
122 ADP PO3 0.428571 0.817073
123 CNA 0.428571 0.855422
124 M24 0.427632 0.806818
125 A4P 0.427586 0.822222
126 MYR AMP 0.426471 0.83908
127 OMR 0.423611 0.850575
128 VO4 ADP 0.423077 0.809524
129 ADP VO4 0.423077 0.809524
130 NAD 0.422819 0.853659
131 ADJ 0.421769 0.894118
132 DSZ 0.421053 0.763441
133 LSS 0.421053 0.729167
134 7MC 0.42069 0.905882
135 VMS 0.419847 0.715789
136 54H 0.419847 0.715789
137 JB6 0.419118 0.857143
138 GJV 0.418033 0.755814
139 NVA LMS 0.41791 0.739583
140 5CA 0.416667 0.763441
141 6RE 0.416667 0.744186
142 TSB 0.416667 0.723404
143 53H 0.416667 0.708333
144 FB0 0.416149 0.846154
145 ADP ALF 0.415385 0.761364
146 A5A 0.415385 0.731183
147 ALF ADP 0.415385 0.761364
148 G5A 0.414062 0.782609
149 139 0.412162 0.892857
150 GSU 0.411765 0.782609
151 NSS 0.410448 0.744681
152 J7C 0.409836 0.752941
153 LPA AMP 0.409722 0.83908
154 LMS 0.408333 0.728261
155 A3D 0.407895 0.843373
156 UP5 0.406897 0.845238
157 TAD 0.405594 0.816092
158 LEU LMS 0.404412 0.721649
159 K15 0.404412 0.770115
160 AMP DBH 0.404255 0.8
161 NAQ 0.403846 0.804598
162 SFG 0.401575 0.777778
163 5X8 0.401575 0.746988
164 SMM 0.401515 0.714286
165 DZD 0.401316 0.880952
166 5AS 0.4 0.744681
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
APoc FAQ
Feedback