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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: 256
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 0.920455
16 G5A 0.738095 0.97619
17 LEU LMS 0.733333 0.920455
18 WSA 0.7 0.964286
19 8X1 0.688889 0.942529
20 5AS 0.686747 0.908046
21 8PZ 0.659794 0.97619
22 LMS 0.654321 0.939759
23 P5A 0.652632 0.931818
24 AHX 0.631579 0.848837
25 8Q2 0.598131 0.942529
26 4YB 0.596154 0.931035
27 SRP 0.595745 0.835294
28 649 0.588785 0.910112
29 SON 0.58427 0.793103
30 A 0.576471 0.776471
31 AMP 0.576471 0.776471
32 5AL 0.574468 0.790698
33 5X8 0.571429 0.729412
34 BA3 0.561798 0.8
35 CA0 0.56044 0.802326
36 ABM 0.556818 0.758621
37 A2D 0.556818 0.8
38 B4P 0.555556 0.8
39 AP5 0.555556 0.8
40 SRA 0.551724 0.802326
41 AN2 0.549451 0.811765
42 A3S 0.549451 0.771084
43 AOC 0.545455 0.697674
44 AP2 0.544444 0.793103
45 A12 0.544444 0.793103
46 XYA 0.544304 0.73494
47 RAB 0.544304 0.73494
48 ADN 0.544304 0.73494
49 ADX 0.543478 0.916667
50 AU1 0.543478 0.802326
51 5CD 0.54321 0.682353
52 XAH 0.542857 0.8
53 AMO 0.54 0.835294
54 SLU 0.538462 0.897727
55 ADP 0.538462 0.8
56 HEJ 0.537634 0.8
57 ATP 0.537634 0.8
58 SAH 0.536842 0.712644
59 3DH 0.534884 0.678161
60 NB8 0.533981 0.827586
61 AT4 0.532609 0.813953
62 AQP 0.531915 0.8
63 5FA 0.531915 0.8
64 GAP 0.53125 0.781609
65 5N5 0.530864 0.714286
66 9ZA 0.53 0.775281
67 9ZD 0.53 0.775281
68 8QN 0.53 0.790698
69 M33 0.526882 0.790698
70 SA8 0.526316 0.663043
71 AGS 0.526316 0.825581
72 SAP 0.526316 0.825581
73 A4D 0.52439 0.73494
74 LAD 0.524272 0.797753
75 50T 0.521277 0.770115
76 ACP 0.521277 0.802326
77 SFG 0.521277 0.697674
78 DAL AMP 0.52 0.770115
79 DLL 0.519608 0.790698
80 ME8 0.519231 0.78022
81 TXA 0.519231 0.793103
82 DTA 0.517647 0.709302
83 AR6 0.515789 0.8
84 PRX 0.515789 0.741573
85 APC 0.515789 0.793103
86 APR 0.515789 0.8
87 TAT 0.515464 0.813953
88 ANP 0.515464 0.802326
89 T99 0.515464 0.813953
90 OOB 0.514852 0.790698
91 3UK 0.514563 0.781609
92 7MD 0.513761 0.820225
93 ADP PO3 0.510417 0.776471
94 RBY 0.510417 0.793103
95 ADV 0.510417 0.793103
96 AD9 0.510417 0.781609
97 4AD 0.509804 0.825581
98 PAJ 0.509804 0.777778
99 0UM 0.509804 0.673913
100 EP4 0.505882 0.644444
101 SAI 0.505155 0.685393
102 ATF 0.50505 0.772727
103 00A 0.504854 0.755556
104 9K8 0.504762 0.760417
105 FA5 0.504673 0.813953
106 YAP 0.504673 0.804598
107 ACQ 0.5 0.802326
108 SAM 0.5 0.684783
109 SMM 0.5 0.680851
110 A7D 0.5 0.72093
111 S7M 0.5 0.684783
112 M2T 0.5 0.666667
113 6YZ 0.5 0.802326
114 6RE 0.5 0.688889
115 9SN 0.495327 0.747253
116 WAQ 0.495238 0.775281
117 B5V 0.495238 0.772727
118 EEM 0.494949 0.648936
119 MTA 0.494253 0.678161
120 FYA 0.490566 0.790698
121 PTJ 0.490566 0.747253
122 MAP 0.490196 0.784091
123 A22 0.490196 0.790698
124 ADP ALF 0.49 0.725275
125 ALF ADP 0.49 0.725275
126 A3N 0.48913 0.689655
127 J7C 0.48913 0.696629
128 YLP 0.486726 0.763441
129 ARG AMP 0.486486 0.752688
130 K15 0.485714 0.642105
131 OAD 0.485714 0.802326
132 25A 0.485437 0.77907
133 ADP VO4 0.485149 0.770115
134 VO4 ADP 0.485149 0.770115
135 GJV 0.483871 0.681319
136 PR8 0.481132 0.788889
137 ADQ 0.480769 0.802326
138 A1R 0.480769 0.816092
139 DSH 0.478261 0.696629
140 TYM 0.478261 0.813953
141 B5Y 0.477064 0.764045
142 B5M 0.477064 0.764045
143 1ZZ 0.476636 0.723404
144 BIS 0.476636 0.755556
145 3OD 0.476636 0.802326
146 62X 0.47619 0.628866
147 A3T 0.474227 0.738095
148 YLB 0.474138 0.763441
149 YLC 0.474138 0.78022
150 48N 0.473684 0.786517
151 ZAS 0.472527 0.693182
152 MYR AMP 0.472222 0.705263
153 25L 0.472222 0.790698
154 9X8 0.471698 0.804598
155 ADP BMA 0.471698 0.781609
156 5SV 0.471154 0.709677
157 TYR AMP 0.468468 0.784091
158 AMP DBH 0.468468 0.741573
159 S4M 0.468085 0.663158
160 A3R 0.466667 0.816092
161 F2R 0.466667 0.782609
162 7C5 0.464286 0.7
163 MAO 0.463158 0.709677
164 JB6 0.462963 0.795455
165 SXZ 0.462963 0.684783
166 NEC 0.462366 0.674419
167 A3G 0.462366 0.761905
168 YLA 0.462185 0.763441
169 7MC 0.461538 0.802198
170 VRT 0.46 0.735632
171 KB1 0.458716 0.655914
172 AYB 0.458333 0.755319
173 TAD 0.45614 0.797753
174 DQV 0.45614 0.811765
175 4UV 0.455357 0.764045
176 IOT 0.453782 0.755319
177 A A 0.453704 0.758621
178 TXE 0.452991 0.775281
179 EO7 0.452632 0.896552
180 LAQ 0.452174 0.76087
181 MHZ 0.44898 0.673684
182 LPA AMP 0.448276 0.741935
183 D3Y 0.447619 0.752941
184 4UU 0.447368 0.764045
185 GA7 0.447368 0.793103
186 AFH 0.447368 0.777778
187 5AD 0.445783 0.630952
188 3AM 0.445652 0.764706
189 6V0 0.444444 0.766667
190 TXD 0.444444 0.775281
191 NAX 0.444444 0.788889
192 DND 0.444444 0.793103
193 2VA 0.444444 0.72093
194 NXX 0.444444 0.793103
195 KH3 0.443478 0.652632
196 GTA 0.443478 0.741935
197 S8M 0.443396 0.727273
198 GEK 0.443396 0.727273
199 Y3J 0.44186 0.616279
200 OMR 0.440678 0.734043
201 AF3 ADP 3PG 0.440678 0.73913
202 7D7 0.440476 0.651163
203 3NZ 0.440367 0.747126
204 AHZ 0.439655 0.723404
205 7D5 0.43956 0.727273
206 COD 0.439024 0.776596
207 G3A 0.438596 0.766667
208 ATP A A A 0.4375 0.767442
209 594 0.436508 0.833333
210 A5D 0.435644 0.709302
211 AR6 AR6 0.434783 0.758621
212 G5P 0.434783 0.766667
213 BS5 0.434426 0.83871
214 N0B 0.434109 0.763441
215 YLY 0.433071 0.755319
216 A2P 0.43299 0.764706
217 A3P 0.43299 0.776471
218 NAI 0.432203 0.775281
219 UP5 0.432203 0.784091
220 4UW 0.432203 0.73913
221 80F 0.432 0.782609
222 SO8 0.431373 0.712644
223 BT5 0.424 0.755319
224 AAT 0.423077 0.681319
225 CNA 0.422764 0.813953
226 NVA 2AD 0.421569 0.727273
227 A4P 0.421488 0.747368
228 7D4 0.42 0.75
229 2AM 0.419355 0.776471
230 NAD 0.416 0.790698
231 AMP NAD 0.416 0.770115
232 T5A 0.414634 0.763441
233 V3L 0.413462 0.77907
234 4TC 0.413223 0.786517
235 AP0 0.413223 0.747253
236 UPA 0.413223 0.795455
237 2A5 0.411765 0.781609
238 590 0.410448 0.84375
239 PPS 0.409524 0.894118
240 A3D 0.409449 0.781609
241 7D3 0.408163 0.75
242 PAP 0.407767 0.788235
243 ATR 0.407767 0.776471
244 NAJ PZO 0.40625 0.747253
245 OVE 0.40625 0.790698
246 2SA 0.40566 0.813953
247 A6D 0.405405 0.677419
248 BTX 0.404762 0.763441
249 NAQ 0.40458 0.747253
250 3AD 0.404494 0.722892
251 139 0.403226 0.788889
252 ADJ 0.403226 0.734043
253 F0P 0.401639 0.681319
254 DZD 0.401575 0.777778
255 M24 0.4 0.75
256 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 with APoc: 67
This union binding pocket(no: 1) in the query (biounit: 2cj9.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1E1O LYS 1.5873
2 1G51 AMO 1.72414
3 4YDQ ANP 1.81087
4 4YDQ HFG 1.81087
5 3NEM ATP 1.82648
6 3NEM AMO 1.82648
7 5VAD 91Y 2.13178
8 5VAD PRO 2.13178
9 2JLD AG1 2.38095
10 4L80 OXL 2.58621
11 3T4L ZEA 2.59259
12 12AS AMP 2.72727
13 1QM5 GLC GLC GLC PO4 SGC GLC 2.87356
14 5X8G S0N 2.8866
15 6EK3 OUL 3.16742
16 2XZ9 PYR 3.39506
17 2ZTG A5A 3.44828
18 3TEG DAH 3.83142
19 1HSK FAD 3.98773
20 3K0T BGC 4.1958
21 3G1Z AMP 4.29448
22 5V59 8X1 4.42105
23 2XGT NSS 4.5977
24 3BJU ATP 4.60653
25 4CS4 ANP 4.74453
26 4CS4 AXZ 4.74453
27 3HXU A5A 4.7619
28 2ART LPA AMP 4.96183
29 2YIP YIO 5.07246
30 5YJS SAL 5.12821
31 3E9I XAH 5.67951
32 1B7Y FYA 5.74713
33 1YFS ALA 6.02151
34 3A5Y KAA 6.08696
35 2Q1A 2KT 6.14334
36 5ACM MBT 6.30631
37 3X27 TRP 6.56716
38 3REU ATP 7.14286
39 1X54 4AD 7.14286
40 2J5B TYE 7.18391
41 5XIJ ANP 7.6
42 5XIJ 873 7.6
43 1TQP ATP 7.80142
44 1M6P M6P 7.89474
45 1VA6 ADP 7.91506
46 3A5Z KAA 8.37696
47 2J3M ATP 8.42912
48 2J3M PRI 8.42912
49 1DCP HBI 8.65385
50 2Y91 98J 8.67924
51 1I7A FLC 9.00901
52 2Y2B AH0 9.62567
53 2I4O ATP 10.0437
54 3IAL PR8 10.8108
55 3UH0 TSB 12.8261
56 3ERR AMP 12.8352
57 4HWT 1B2 14.2857
58 4HWS 1B3 16.0584
59 1NU4 MLA 16.4948
60 5XIO ANP 16.6667
61 5XIO HFG 16.6667
62 3ZGE ASP 18.1992
63 4H2V AMP 29.7688
64 3MF2 AMP 29.7688
65 4H2X G5A 30.0578
66 4H2W AMP 30.0578
67 4H2W 5GP 30.0578
Pocket No.: 2; Query (leader) PDB : 2CJ9; Ligand: SSA; Similar sites found with APoc: 14
This union binding pocket(no: 2) in the query (biounit: 2cj9.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4EE7 PIS 1.64474
2 4N70 2HX 1.82927
3 2CYB TYR 1.85759
4 1Q19 SSC 1.98807
5 3MTX PGT 2.64901
6 5XDT MB3 2.92208
7 3ROE THM 3.39623
8 1P7L ANP 3.91645
9 2Z77 HE7 5.03597
10 1RP7 TZD 5.17241
11 4NAO AKG 5.82822
12 4QTB 38Z 8.94737
13 5LXT GTP 9.53437
14 2BOS GLA GAL 10.2941
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