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
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: YLY; Similar ligands found: 186
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 FA5 0.581967 0.86747
16 8QN 0.581197 0.865854
17 CA0 0.567568 0.833333
18 4AD 0.563025 0.857143
19 PAJ 0.563025 0.848837
20 PTJ 0.557377 0.837209
21 PR8 0.54918 0.951219
22 TYM 0.541985 0.86747
23 XAH 0.539683 0.894118
24 TXA 0.532258 0.845238
25 AT4 0.530973 0.781609
26 F2R 0.529412 0.873563
27 M33 0.526316 0.821429
28 A1R 0.52459 0.891566
29 WAQ 0.524194 0.914634
30 A2D 0.522523 0.809524
31 DLL 0.520325 0.843373
32 AHX 0.520325 0.837209
33 1ZZ 0.52 0.939759
34 AN2 0.517544 0.8
35 PRX 0.517241 0.855422
36 ANP 0.516949 0.790698
37 3UK 0.516129 0.833333
38 BA3 0.513274 0.809524
39 ABM 0.508929 0.831325
40 AP5 0.508772 0.809524
41 B4P 0.508772 0.809524
42 ADP 0.508772 0.809524
43 3OD 0.507937 0.855422
44 IOT 0.507353 0.906977
45 AR6 0.504274 0.831325
46 APR 0.504274 0.831325
47 OOB 0.504065 0.843373
48 ADX 0.5 0.73913
49 9SN 0.5 0.795455
50 AU1 0.5 0.790698
51 A3R 0.5 0.891566
52 B5V 0.5 0.823529
53 LAQ 0.496241 0.850575
54 B5Y 0.496124 0.835294
55 00A 0.496 0.804598
56 50T 0.495726 0.77907
57 ACP 0.495726 0.811765
58 HEJ 0.495726 0.809524
59 ATP 0.495726 0.809524
60 A 0.495495 0.807229
61 AMP 0.495495 0.807229
62 ARG AMP 0.492424 0.862069
63 9ZA 0.491935 0.825581
64 9ZD 0.491935 0.825581
65 5SV 0.491935 0.903614
66 AQP 0.491525 0.809524
67 5FA 0.491525 0.809524
68 SAP 0.487395 0.772727
69 AD9 0.487395 0.790698
70 AGS 0.487395 0.772727
71 B5M 0.484615 0.835294
72 FYA 0.484375 0.843373
73 DAL AMP 0.483871 0.843373
74 4UU 0.481203 0.813953
75 OAD 0.480315 0.855422
76 ACQ 0.479339 0.811765
77 BT5 0.478873 0.863636
78 NAI 0.477941 0.784091
79 4UW 0.477941 0.827586
80 ADQ 0.47619 0.833333
81 A12 0.474138 0.823529
82 AP2 0.474138 0.823529
83 8X1 0.472 0.768421
84 COD 0.471831 0.908046
85 ATF 0.471545 0.781609
86 7MD 0.470149 0.916667
87 AFH 0.470149 0.806818
88 9X8 0.46875 0.813953
89 6YZ 0.467742 0.811765
90 T99 0.467213 0.781609
91 GAP 0.467213 0.855422
92 TAT 0.467213 0.781609
93 NAX 0.467153 0.818182
94 4UV 0.466165 0.813953
95 SON 0.466102 0.86747
96 SRA 0.464912 0.770115
97 OMR 0.463768 0.928571
98 ADV 0.46281 0.845238
99 RBY 0.46281 0.845238
100 G3A 0.462687 0.775281
101 BIS 0.461538 0.804598
102 A22 0.460317 0.8
103 MAP 0.460317 0.772727
104 G5P 0.459259 0.775281
105 MYR AMP 0.458015 0.916667
106 25A 0.456693 0.809524
107 GTA 0.455882 0.769231
108 APC 0.454545 0.823529
109 P5A 0.453846 0.817204
110 KAA 0.453846 0.806452
111 TXE 0.453237 0.825581
112 AP0 0.45 0.795455
113 48N 0.449275 0.858824
114 53H 0.448819 0.71875
115 GA7 0.448529 0.845238
116 TXD 0.446043 0.825581
117 DQV 0.445255 0.821429
118 TYR AMP 0.444444 0.835294
119 BTX 0.441379 0.852273
120 54H 0.440945 0.726316
121 VMS 0.440945 0.726316
122 7MC 0.439716 0.940476
123 JB6 0.439394 0.825581
124 ADP PO3 0.439024 0.807229
125 LPA AMP 0.438849 0.829545
126 CNA 0.4375 0.823529
127 TSB 0.4375 0.734043
128 A5A 0.436508 0.741935
129 M24 0.436242 0.777778
130 25L 0.43609 0.8
131 DND 0.435714 0.823529
132 6V0 0.435714 0.795455
133 NXX 0.435714 0.823529
134 80F 0.435374 0.791209
135 FB0 0.433121 0.920455
136 SSA 0.433071 0.755319
137 J7C 0.432203 0.744186
138 GSU 0.431818 0.774194
139 LSS 0.430769 0.757895
140 DSZ 0.430769 0.755319
141 T5A 0.430556 0.831461
142 ADJ 0.430556 0.840909
143 GJV 0.428571 0.747126
144 6RE 0.42735 0.735632
145 A4P 0.426573 0.774194
146 5CA 0.426357 0.755319
147 UP5 0.425532 0.793103
148 ADP ALF 0.425197 0.752809
149 ALF ADP 0.425197 0.752809
150 G5A 0.424 0.774194
151 VO4 ADP 0.421875 0.8
152 SMM 0.421875 0.784091
153 ADP VO4 0.421875 0.8
154 NAD 0.421769 0.821429
155 5AS 0.421488 0.755319
156 139 0.42069 0.83908
157 4TC 0.41958 0.795455
158 UPA 0.41958 0.804598
159 LMS 0.418803 0.72043
160 52H 0.418605 0.71875
161 NVA LMS 0.416667 0.768421
162 A3D 0.416107 0.833333
163 YSA 0.416058 0.736842
164 SA8 0.416 0.809524
165 TAD 0.414286 0.806818
166 K15 0.413534 0.845238
167 AMP DBH 0.413043 0.770115
168 AF3 ADP 3PG 0.412587 0.786517
169 AOC 0.411765 0.705882
170 NAQ 0.411765 0.816092
171 NDC 0.40625 0.858824
172 EEM 0.40625 0.770115
173 62X 0.406015 0.825581
174 NAE 0.405229 0.835294
175 EAD 0.403846 0.797753
176 LEU LMS 0.402985 0.75
177 ADP BMA 0.402985 0.811765
178 0WD 0.402685 0.775281
179 SAI 0.401575 0.752941
180 AHZ 0.401408 0.829545
181 ETB 0.401316 0.886364
182 A A 0.4 0.788235
183 S7M 0.4 0.770115
184 DZD 0.4 0.848837
185 5X8 0.4 0.738095
186 SFG 0.4 0.768293
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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