Receptor
PDB id Resolution Class Description Source Keywords
6H9X 2.1 Å EC: 6.1.1.11 KLEBSIELLA PNEUMONIAE SERYL-TRNA SYNTHETASE IN COMPLEX WITH INTERMEDIATE ANALOG 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE KLEBSIELLA PNEUMONIAE COIL-COIL BETA BARREL TRNA SYNTHETASE COMPLEX LIGASE
Ref.: ACYLATED SULFONAMIDE ADENOSINES AS POTENT INHIBITOR ADENYLATE-FORMING ENZYME SUPERFAMILY. EUR.J.MED.CHEM. V. 174 252 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:507;
A:505;
A:506;
Part of Protein;
Invalid;
Invalid;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
EDO A:502;
A:504;
A:503;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SSA A:501;
Valid;
none;
submit data
433.397 C13 H19 N7 O8 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6R1M 1.5 Å EC: 6.1.1.11 CRYSTAL STRUCTURE OF E. COLI SERYL-TRNA SYNTHETASE COMPLEXED SULFAMOYL ADENOSINE ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE CLASS II PROTEIN SYNTHESIS INHILIGASE
Ref.: STRUCTURE-GUIDED ENHANCEMENT OF SELECTIVITY OF CHEM PROBE INHIBITORS TARGETING BACTERIAL SERYL-TRNA SYN J.MED.CHEM. V. 62 9703 2019
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 7AP1 - RUZ C16 H23 N5 O9 S c1c(cc2c(c....
2 6R1M ic50 = 0.21 uM SSA C13 H19 N7 O8 S c1nc(c2c(n....
3 6H9X - SSA C13 H19 N7 O8 S c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 7AP1 - RUZ C16 H23 N5 O9 S c1c(cc2c(c....
2 6R1M ic50 = 0.21 uM SSA C13 H19 N7 O8 S c1nc(c2c(n....
3 6H9X - SSA C13 H19 N7 O8 S c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1SES - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 3ERR - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 7AP1 - RUZ C16 H23 N5 O9 S c1c(cc2c(c....
4 6R1M ic50 = 0.21 uM SSA C13 H19 N7 O8 S c1nc(c2c(n....
5 6H9X - SSA C13 H19 N7 O8 S c1nc(c2c(n....
6 6X94 - SSA C13 H19 N7 O8 S c1nc(c2c(n....
7 6R1N ic50 = 0.23 uM SSA C13 H19 N7 O8 S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: SSA; Similar ligands found: 311
No: Ligand ECFP6 Tc MDL keys Tc
1 SSA 1 1
2 5CA 0.876543 1
3 LSS 0.833333 0.931035
4 DSZ 0.833333 0.97619
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 54H 0.797619 0.918605
10 VMS 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 WSA 0.7 0.964286
18 8X1 0.688889 0.942529
19 5AS 0.686747 0.908046
20 8PZ 0.659794 0.97619
21 LMS 0.654321 0.939759
22 P5A 0.652632 0.931818
23 AHX 0.631579 0.848837
24 B1U 0.62 0.858696
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 RUZ 0.587629 0.975904
30 SON 0.58427 0.793103
31 AMP 0.576471 0.776471
32 A 0.576471 0.776471
33 5AL 0.574468 0.790698
34 5X8 0.571429 0.729412
35 AMP MG 0.569767 0.764706
36 BA3 0.561798 0.8
37 CA0 0.56044 0.802326
38 LEU LMS 0.56 0.855556
39 45A 0.556818 0.758621
40 ABM 0.556818 0.758621
41 A2D 0.556818 0.8
42 AP5 0.555556 0.8
43 B4P 0.555556 0.8
44 KG4 0.554348 0.802326
45 SRA 0.551724 0.802326
46 QA7 0.55102 0.764045
47 AN2 0.549451 0.811765
48 A3S 0.549451 0.771084
49 8LH 0.546392 0.793103
50 AOC 0.545455 0.697674
51 A12 0.544444 0.793103
52 AP2 0.544444 0.793103
53 RAB 0.544304 0.73494
54 XYA 0.544304 0.73494
55 ADN 0.544304 0.73494
56 AU1 0.543478 0.802326
57 ADX 0.543478 0.916667
58 5CD 0.54321 0.682353
59 XAH 0.542857 0.8
60 V2G 0.541667 0.806818
61 AMO 0.54 0.835294
62 ADP 0.538462 0.8
63 SLU 0.538462 0.897727
64 HEJ 0.537634 0.8
65 ATP 0.537634 0.8
66 SAH 0.536842 0.712644
67 3DH 0.534884 0.678161
68 NB8 0.533981 0.827586
69 AT4 0.532609 0.813953
70 ADP MG 0.532609 0.776471
71 ADP BEF 0.532609 0.776471
72 5FA 0.531915 0.8
73 AQP 0.531915 0.8
74 GAP 0.53125 0.781609
75 5N5 0.530864 0.714286
76 9ZA 0.53 0.775281
77 9ZD 0.53 0.775281
78 8QN 0.53 0.790698
79 M33 0.526882 0.790698
80 AGS 0.526316 0.825581
81 SA8 0.526316 0.663043
82 8LE 0.525773 0.764045
83 A4D 0.52439 0.73494
84 LAD 0.524272 0.797753
85 ACP 0.521277 0.802326
86 SFG 0.521277 0.697674
87 50T 0.521277 0.770115
88 8LQ 0.52 0.793103
89 DAL AMP 0.52 0.770115
90 DLL 0.519608 0.790698
91 ME8 0.519231 0.78022
92 TXA 0.519231 0.793103
93 DTA 0.517647 0.709302
94 APC 0.515789 0.793103
95 APR 0.515789 0.8
96 PRX 0.515789 0.741573
97 AR6 0.515789 0.8
98 TAT 0.515464 0.813953
99 ANP 0.515464 0.802326
100 T99 0.515464 0.813953
101 QXP 0.514852 0.873563
102 OOB 0.514852 0.790698
103 3UK 0.514563 0.781609
104 7MD 0.513761 0.820225
105 AD9 0.510417 0.781609
106 RBY 0.510417 0.793103
107 ADP PO3 0.510417 0.776471
108 ATP MG 0.510417 0.776471
109 APC MG 0.510417 0.758621
110 ADV 0.510417 0.793103
111 0UM 0.509804 0.673913
112 PAJ 0.509804 0.777778
113 4AD 0.509804 0.825581
114 EP4 0.505882 0.644444
115 H1Q 0.505263 0.767442
116 SAI 0.505155 0.685393
117 BEF ADP 0.505155 0.758621
118 ATF 0.50505 0.772727
119 ANP MG 0.50505 0.790698
120 00A 0.504854 0.755556
121 JNT 0.504854 0.823529
122 9K8 0.504762 0.760417
123 FA5 0.504673 0.813953
124 S7M 0.5 0.684783
125 6YZ 0.5 0.802326
126 A7D 0.5 0.72093
127 M2T 0.5 0.666667
128 6RE 0.5 0.688889
129 RSN 0.5 0.964286
130 SMM 0.5 0.680851
131 SAM 0.5 0.684783
132 RRW 0.5 0.91954
133 ACQ 0.5 0.802326
134 9SN 0.495327 0.747253
135 WAQ 0.495238 0.775281
136 B5V 0.495238 0.772727
137 EEM 0.494949 0.648936
138 MTA 0.494253 0.678161
139 PTJ 0.490566 0.747253
140 FYA 0.490566 0.790698
141 MAP 0.490196 0.784091
142 A22 0.490196 0.790698
143 VO4 ADP 0.49 0.761364
144 ALF ADP 0.49 0.725275
145 J7C 0.48913 0.696629
146 A3N 0.48913 0.689655
147 NWW 0.488095 0.662651
148 YLP 0.486726 0.763441
149 ARG AMP 0.486486 0.752688
150 K15 0.485714 0.642105
151 QXG 0.485714 0.863636
152 OAD 0.485714 0.802326
153 25A 0.485437 0.77907
154 GJV 0.483871 0.681319
155 J4G 0.481132 0.804598
156 PR8 0.481132 0.788889
157 R2V 0.481132 0.873563
158 ADQ 0.480769 0.802326
159 A1R 0.480769 0.816092
160 HQG 0.480392 0.790698
161 DSH 0.478261 0.696629
162 TYM 0.478261 0.813953
163 B5Y 0.477064 0.764045
164 B5M 0.477064 0.764045
165 1ZZ 0.476636 0.723404
166 BIS 0.476636 0.755556
167 3OD 0.476636 0.802326
168 62X 0.47619 0.628866
169 A3T 0.474227 0.738095
170 YLB 0.474138 0.763441
171 YLC 0.474138 0.78022
172 48N 0.473684 0.786517
173 ZAS 0.472527 0.693182
174 25L 0.472222 0.790698
175 MYR AMP 0.472222 0.705263
176 ADP BMA 0.471698 0.781609
177 9X8 0.471698 0.804598
178 OZV 0.471154 0.8
179 5SV 0.471154 0.709677
180 RRB 0.469027 0.941176
181 AMP DBH 0.468468 0.741573
182 S4M 0.468085 0.663158
183 A3R 0.466667 0.816092
184 F2R 0.466667 0.782609
185 7C5 0.464286 0.7
186 MAO 0.463158 0.709677
187 JB6 0.462963 0.795455
188 SXZ 0.462963 0.684783
189 NEC 0.462366 0.674419
190 A3G 0.462366 0.761905
191 YLA 0.462185 0.763441
192 7MC 0.461538 0.802198
193 VRT 0.46 0.735632
194 KYE 0.459459 0.670213
195 KB1 0.458716 0.655914
196 AYB 0.458333 0.755319
197 KXW 0.45614 0.681319
198 TAD 0.45614 0.797753
199 DQV 0.45614 0.811765
200 4UV 0.455357 0.764045
201 IOT 0.453782 0.755319
202 ALF ADP 3PG 0.452991 0.73913
203 TXE 0.452991 0.775281
204 EO7 0.452632 0.896552
205 LAQ 0.452174 0.76087
206 HZ2 0.452174 0.703297
207 NWQ 0.450549 0.647059
208 KMQ 0.45045 0.772727
209 MHZ 0.44898 0.673684
210 KOY 0.448276 0.704545
211 LPA AMP 0.448276 0.741935
212 D3Y 0.447619 0.752941
213 GA7 0.447368 0.793103
214 AFH 0.447368 0.777778
215 4UU 0.447368 0.764045
216 N5O 0.446809 0.729412
217 5AD 0.445783 0.630952
218 3AM 0.445652 0.764706
219 DND 0.444444 0.793103
220 6V0 0.444444 0.766667
221 2VA 0.444444 0.72093
222 HY8 0.444444 0.703297
223 NAX 0.444444 0.788889
224 TXD 0.444444 0.775281
225 GTA 0.443478 0.741935
226 KH3 0.443478 0.652632
227 S8M 0.443396 0.727273
228 GEK 0.443396 0.727273
229 V47 0.442308 0.686047
230 Y3J 0.44186 0.616279
231 OMR 0.440678 0.734043
232 AF3 ADP 3PG 0.440678 0.73913
233 7D7 0.440476 0.651163
234 3NZ 0.440367 0.747126
235 AHZ 0.439655 0.723404
236 7D5 0.43956 0.727273
237 COD 0.439024 0.776596
238 G3A 0.438596 0.766667
239 ATP A 0.4375 0.767442
240 N5A 0.4375 0.705882
241 ATP A A A 0.4375 0.767442
242 NAD IBO 0.436975 0.77907
243 NAD TDB 0.436975 0.77907
244 594 0.436508 0.833333
245 U4Y 0.435897 0.707865
246 A5D 0.435644 0.709302
247 AR6 AR6 0.434783 0.758621
248 G5P 0.434783 0.766667
249 BS5 0.434426 0.83871
250 N0B 0.434109 0.763441
251 YLY 0.433071 0.755319
252 A3P 0.43299 0.776471
253 A2P 0.43299 0.764706
254 NAI 0.432203 0.775281
255 EU9 0.432203 0.697917
256 UP5 0.432203 0.784091
257 4UW 0.432203 0.73913
258 80F 0.432 0.782609
259 SO8 0.431373 0.712644
260 FZQ 0.431373 0.875
261 L3W 0.425 0.793103
262 Q2M 0.425 0.666667
263 Q34 0.425 0.635417
264 K3K 0.424779 0.704545
265 BT5 0.424 0.755319
266 OZP 0.423729 0.681319
267 AAT 0.423077 0.681319
268 CNA 0.422764 0.813953
269 NVA 2AD 0.421569 0.727273
270 A4P 0.421488 0.747368
271 KY2 0.420561 0.666667
272 7D4 0.42 0.75
273 2AM 0.419355 0.776471
274 K3E 0.417391 0.696629
275 AMP NAD 0.416 0.770115
276 NAD 0.416 0.790698
277 Q2V 0.414634 0.655914
278 T5A 0.414634 0.763441
279 K2K 0.414414 0.688889
280 V3L 0.413462 0.77907
281 NX8 0.413462 0.688889
282 UPA 0.413223 0.795455
283 AP0 0.413223 0.747253
284 4TC 0.413223 0.786517
285 KYB 0.412844 0.666667
286 2A5 0.411765 0.781609
287 590 0.410448 0.84375
288 PPS 0.409524 0.894118
289 A3D 0.409449 0.781609
290 7D3 0.408163 0.75
291 6MZ 0.408163 0.747126
292 FZK 0.407767 0.883721
293 PAP 0.407767 0.788235
294 ATR 0.407767 0.776471
295 D4F 0.407692 0.76087
296 NAJ PZO 0.40625 0.747253
297 OVE 0.40625 0.790698
298 2SA 0.40566 0.813953
299 A6D 0.405405 0.677419
300 N37 0.404959 0.685393
301 Q2P 0.404762 0.635417
302 BTX 0.404762 0.763441
303 NAQ 0.40458 0.747253
304 3AD 0.404494 0.722892
305 139 0.403226 0.788889
306 ADJ 0.403226 0.734043
307 F0P 0.401639 0.681319
308 DZD 0.401575 0.777778
309 M24 0.4 0.75
310 FZT 0.4 0.863636
311 67D 0.4 0.909091
Similar Ligands (3D)
Ligand no: 1; Ligand: SSA; Similar ligands found: 9
No: Ligand Similarity coefficient
1 GDP 0.9052
2 3AT 0.8856
3 DTP 0.8856
4 GNP 0.8828
5 GDP MG 0.8731
6 GTP 0.8728
7 CDP 0.8707
8 GCP 0.8643
9 GNH 0.8577
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6R1M; Ligand: SSA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6r1m.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6R1M; Ligand: SSA; 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: 6r1m.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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