Receptor
PDB id Resolution Class Description Source Keywords
2CJ9 2.3 Å EC: 6.1.1.11 CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH AN ANALOG OF SERYLADENYLATE METHANOSARCINA BARKERI LIGASE ZINC ION SERYLADENYLATE TRNA SYNTHETASE
Ref.: STRUCTURE OF THE UNUSUAL SERYL-TRNA SYNTHETASE REVE DISTINCT ZINC-DEPENDENT MODE OF SUBSTRATE RECOGNITI EMBO J. V. 25 2498 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:1504;
B:1504;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
SSA A:1505;
B:1505;
Valid;
Valid;
none;
none;
submit data
433.397 C13 H19 N7 O8 S c1nc(...
ZN A:1503;
B:1503;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CJ9 2.3 Å EC: 6.1.1.11 CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH AN ANALOG OF SERYLADENYLATE METHANOSARCINA BARKERI LIGASE ZINC ION SERYLADENYLATE TRNA SYNTHETASE
Ref.: STRUCTURE OF THE UNUSUAL SERYL-TRNA SYNTHETASE REVE DISTINCT ZINC-DEPENDENT MODE OF SUBSTRATE RECOGNITI EMBO J. V. 25 2498 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2CJ9 - SSA C13 H19 N7 O8 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2CJ9 - SSA C13 H19 N7 O8 S c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2CJ9 - SSA C13 H19 N7 O8 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SSA; Similar ligands found: 241
No: Ligand ECFP6 Tc MDL keys Tc
1 SSA 1 1
2 5CA 0.876543 1
3 DSZ 0.833333 0.97619
4 LSS 0.833333 0.931035
5 A5A 0.817073 0.940476
6 53H 0.809524 0.908046
7 KAA 0.804598 0.942529
8 GSU 0.804598 0.952941
9 VMS 0.797619 0.918605
10 54H 0.797619 0.918605
11 TSB 0.788235 0.952381
12 52H 0.776471 0.908046
13 YSA 0.76087 0.952941
14 NSS 0.75 0.97619
15 NVA LMS 0.741573 0.909091
16 G5A 0.738095 0.97619
17 LEU LMS 0.733333 0.909091
18 WSA 0.7 0.964286
19 5AS 0.686747 0.908046
20 P5A 0.652632 0.931818
21 AHX 0.631579 0.848837
22 4YB 0.596154 0.931035
23 SRP 0.595745 0.835294
24 649 0.588785 0.910112
25 SON 0.58427 0.793103
26 AMP 0.576471 0.776471
27 A 0.576471 0.776471
28 5AL 0.574468 0.790698
29 5X8 0.571429 0.729412
30 AMP MG 0.563218 0.738636
31 BA3 0.561798 0.8
32 CA0 0.56044 0.802326
33 ABM 0.556818 0.758621
34 A2D 0.556818 0.8
35 B4P 0.555556 0.8
36 AP5 0.555556 0.8
37 SRA 0.551724 0.802326
38 AN2 0.549451 0.811765
39 A3S 0.549451 0.771084
40 AOC 0.545455 0.697674
41 AP2 0.544444 0.793103
42 A12 0.544444 0.793103
43 RAB 0.544304 0.73494
44 ADN 0.544304 0.73494
45 XYA 0.544304 0.73494
46 ADX 0.543478 0.916667
47 AU1 0.543478 0.802326
48 5CD 0.54321 0.682353
49 XAH 0.542857 0.8
50 AMO 0.54 0.835294
51 SLU 0.538462 0.897727
52 ADP 0.538462 0.8
53 ATP 0.537634 0.8
54 SAH 0.536842 0.712644
55 3DH 0.534884 0.678161
56 NB8 0.533981 0.827586
57 AQP 0.531915 0.8
58 5FA 0.531915 0.8
59 GAP 0.53125 0.781609
60 5N5 0.530864 0.714286
61 8QN 0.53 0.790698
62 M33 0.526882 0.790698
63 ADP MG 0.526882 0.75
64 SA8 0.526316 0.663043
65 SAP 0.526316 0.825581
66 AGS 0.526316 0.825581
67 A4D 0.52439 0.73494
68 LAD 0.524272 0.797753
69 BEF ADP 0.521277 0.733333
70 ADP BEF 0.521277 0.733333
71 50T 0.521277 0.770115
72 SFG 0.521277 0.697674
73 ACP 0.521277 0.802326
74 DAL AMP 0.52 0.770115
75 DLL 0.519608 0.790698
76 TXA 0.519231 0.793103
77 ME8 0.519231 0.78022
78 DTA 0.517647 0.709302
79 AR6 0.515789 0.8
80 APR 0.515789 0.8
81 PRX 0.515789 0.741573
82 APC 0.515789 0.793103
83 ANP 0.515464 0.802326
84 TAT 0.515464 0.813953
85 OOB 0.514852 0.790698
86 3UK 0.514563 0.781609
87 7MD 0.513761 0.820225
88 ADP PO3 0.510417 0.776471
89 AD9 0.510417 0.781609
90 RBY 0.510417 0.793103
91 ADV 0.510417 0.793103
92 0UM 0.509804 0.673913
93 PAJ 0.509804 0.777778
94 4AD 0.509804 0.825581
95 EP4 0.505882 0.644444
96 SAI 0.505155 0.685393
97 ATP MG 0.505155 0.75
98 ATF 0.50505 0.772727
99 00A 0.504854 0.755556
100 YAP 0.504673 0.804598
101 FA5 0.504673 0.813953
102 M2T 0.5 0.666667
103 ACQ 0.5 0.802326
104 SAM 0.5 0.684783
105 A7D 0.5 0.72093
106 SMM 0.5 0.680851
107 6RE 0.5 0.688889
108 ANP MG 0.5 0.764045
109 S7M 0.5 0.684783
110 9SN 0.495327 0.747253
111 WAQ 0.495238 0.775281
112 EEM 0.494949 0.648936
113 MTA 0.494253 0.678161
114 PTJ 0.490566 0.747253
115 FYA 0.490566 0.790698
116 MAP 0.490196 0.784091
117 A22 0.490196 0.790698
118 ALF ADP 0.49 0.725275
119 ADP ALF 0.49 0.725275
120 J7C 0.48913 0.696629
121 A3N 0.48913 0.689655
122 YLP 0.486726 0.763441
123 OAD 0.485714 0.802326
124 K15 0.485714 0.642105
125 25A 0.485437 0.77907
126 VO4 ADP 0.485149 0.770115
127 ADP VO4 0.485149 0.770115
128 GJV 0.483871 0.681319
129 PR8 0.481132 0.788889
130 A1R 0.480769 0.816092
131 ADQ 0.480769 0.802326
132 DSH 0.478261 0.696629
133 TYM 0.478261 0.813953
134 ARG AMP 0.477876 0.752688
135 3OD 0.476636 0.802326
136 BIS 0.476636 0.755556
137 1ZZ 0.476636 0.723404
138 62X 0.47619 0.628866
139 A3T 0.474227 0.738095
140 YLC 0.474138 0.78022
141 YLB 0.474138 0.763441
142 48N 0.473684 0.786517
143 TYR AMP 0.472727 0.772727
144 ZAS 0.472527 0.693182
145 MYR AMP 0.472222 0.705263
146 25L 0.472222 0.790698
147 ADP BMA 0.471698 0.781609
148 5SV 0.471154 0.709677
149 AMP DBH 0.468468 0.741573
150 S4M 0.468085 0.663158
151 7C5 0.464286 0.7
152 MAO 0.463158 0.709677
153 JB6 0.462963 0.795455
154 SXZ 0.462963 0.684783
155 A3G 0.462366 0.761905
156 NEC 0.462366 0.674419
157 YLA 0.462185 0.763441
158 7MC 0.461538 0.802198
159 VRT 0.46 0.735632
160 KB1 0.458716 0.655914
161 AYB 0.458333 0.755319
162 TAD 0.45614 0.797753
163 4UV 0.455357 0.764045
164 IOT 0.453782 0.755319
165 A A 0.453704 0.758621
166 ALF ADP 3PG 0.452991 0.73913
167 LA8 ALF 3PG 0.452991 0.73913
168 TXE 0.452991 0.775281
169 LAQ 0.452174 0.76087
170 MHZ 0.44898 0.673684
171 LPA AMP 0.448276 0.741935
172 D3Y 0.447619 0.752941
173 4UU 0.447368 0.764045
174 AFH 0.447368 0.777778
175 5AD 0.445783 0.630952
176 3AM 0.445652 0.764706
177 DND 0.444444 0.793103
178 NAX 0.444444 0.788889
179 6V0 0.444444 0.766667
180 TXD 0.444444 0.775281
181 NXX 0.444444 0.793103
182 2VA 0.444444 0.72093
183 KH3 0.443478 0.652632
184 GTA 0.443478 0.741935
185 S8M 0.443396 0.727273
186 GEK 0.443396 0.727273
187 Y3J 0.44186 0.616279
188 OMR 0.440678 0.734043
189 AF3 ADP 3PG 0.440678 0.73913
190 7D7 0.440476 0.651163
191 3NZ 0.440367 0.747126
192 AHZ 0.439655 0.723404
193 7D5 0.43956 0.727273
194 COD 0.439024 0.776596
195 G3A 0.438596 0.766667
196 ATP A A A 0.4375 0.767442
197 594 0.436508 0.833333
198 A5D 0.435644 0.709302
199 G5P 0.434783 0.766667
200 AR6 AR6 0.434783 0.758621
201 BS5 0.434426 0.83871
202 N0B 0.434109 0.763441
203 YLY 0.433071 0.755319
204 A3P 0.43299 0.776471
205 A2P 0.43299 0.764706
206 NAI 0.432203 0.775281
207 4UW 0.432203 0.73913
208 UP5 0.432203 0.784091
209 SO8 0.431373 0.712644
210 NAD IBO 0.430894 0.744444
211 BT5 0.424 0.755319
212 AAT 0.423077 0.681319
213 CNA 0.422764 0.813953
214 A4P 0.421488 0.747368
215 7D4 0.42 0.75
216 2AM 0.419355 0.776471
217 NAD 0.416 0.790698
218 T5A 0.414634 0.763441
219 V3L 0.413462 0.77907
220 4TC 0.413223 0.786517
221 UPA 0.413223 0.795455
222 AP0 0.413223 0.747253
223 2A5 0.411765 0.781609
224 590 0.410448 0.84375
225 PPS 0.409524 0.894118
226 A3D 0.409449 0.781609
227 7D3 0.408163 0.75
228 PAP 0.407767 0.788235
229 ATR 0.407767 0.776471
230 OVE 0.40625 0.790698
231 NAJ PZO 0.40625 0.747253
232 2SA 0.40566 0.813953
233 A6D 0.405405 0.677419
234 BTX 0.404762 0.763441
235 NAQ 0.40458 0.747253
236 3AD 0.404494 0.722892
237 ADJ 0.403226 0.734043
238 139 0.403226 0.788889
239 DZD 0.401575 0.777778
240 M24 0.4 0.75
241 67D 0.4 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CJ9; Ligand: SSA; Similar sites found: 51
This union binding pocket(no: 1) in the query (biounit: 2cj9.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1E1O LYS 0.000002751 0.49494 1.5873
2 1G51 AMO 0.000009433 0.4719 1.72414
3 4YDQ HFG 0.0000003658 0.40674 1.81087
4 4YDQ ANP 0.0000003895 0.40289 1.81087
5 3NEM ATP 0.0000004206 0.62279 1.82648
6 3NEM AMO 0.00000005253 0.54975 1.82648
7 5VAD 91Y 0.0000002058 0.49283 2.13178
8 5VAD PRO 0.005112 0.41733 2.13178
9 4L80 OXL 0.02548 0.40178 2.58621
10 3T4L ZEA 0.003367 0.41758 2.59259
11 3MTX PGT 0.01404 0.40327 2.64901
12 12AS AMP 0.000003316 0.48451 2.72727
13 1RZM PEP 0.0214 0.40401 2.95858
14 2ZTG A5A 0.00000004367 0.63194 3.44828
15 3TEG DAH 0.001391 0.42305 3.83142
16 3K0T BGC 0.02871 0.4016 4.1958
17 3G1Z AMP 0.000003804 0.57672 4.29448
18 2XGT NSS 0.0000004487 0.51633 4.5977
19 3BJU ATP 0.00008121 0.49994 4.60653
20 4CS4 ANP 0.0000006551 0.44801 4.74453
21 4CS4 AXZ 0.0000009212 0.41922 4.74453
22 3HXU A5A 0.00000004493 0.58768 4.7619
23 3E9I XAH 0.0000003652 0.50364 5.67951
24 1B7Y FYA 0.000006202 0.48178 5.74713
25 1YFS ALA 0.00007053 0.52697 6.02151
26 3A5Y KAA 0.000001029 0.51877 6.08696
27 2Q1A 2KT 0.02529 0.40278 6.14334
28 3X27 TRP 0.003924 0.43638 6.56716
29 1X54 4AD 0.0000009526 0.57945 7.14286
30 3REU ATP 0.0000008791 0.57476 7.14286
31 2J5B TYE 0.02385 0.40232 7.18391
32 1M6P M6P 0.01946 0.40612 7.89474
33 3A5Z KAA 0.000001944 0.50093 8.37696
34 2J3M ATP 0.00000006278 0.58067 8.42912
35 2J3M PRI 0.00000008277 0.56599 8.42912
36 1DCP HBI 0.04596 0.4054 8.65385
37 2Y91 98J 0.007157 0.44739 8.67924
38 2Y2B AH0 0.02292 0.40471 9.62567
39 2I4O ATP 0.0000002612 0.63276 10.0437
40 3IAL PR8 0.000000003184 0.62889 10.8108
41 3UH0 TSB 0.000000198 0.54984 12.8261
42 3ERR AMP 0.00001818 0.48718 12.8352
43 4HWT 1B2 0.002024 0.42333 14.2857
44 4HWS 1B3 0.0000004949 0.45393 16.0584
45 1NU4 MLA 0.02041 0.43082 16.4948
46 3ZGE ASP 0.007491 0.42391 18.1992
47 4H2V AMP 0.000000008882 0.6248 29.7688
48 3MF2 AMP 0.0000000143 0.60438 29.7688
49 4H2X G5A 0.000000004526 0.66583 30.0578
50 4H2W AMP 0.0000001827 0.61285 30.0578
51 4H2W 5GP 0.000001597 0.56339 30.0578
Pocket No.: 2; Query (leader) PDB : 2CJ9; Ligand: SSA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2cj9.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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