Receptor
PDB id Resolution Class Description Source Keywords
2Y4O 1.9 Å EC: 6.2.1.30 CRYSTAL STRUCTURE OF PAAK2 IN COMPLEX WITH PHENYLACETYL ADEN BURKHOLDERIA CENOCEPACIA LIGASE PHENYLACETIC ACID DEGRADATION PATHWAY
Ref.: DEFINING A STRUCTURAL AND KINETIC RATIONALE FOR PARALOGOUS COPIES OF PHENYLACETATE-COA LIGASES FROM THE CYSTIC FIBROSIS PATHOGEN BURKHOLDERIA CENOCEPACIA J2315. J.BIOL.CHEM. V. 286 15577 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME B:1444;
Invalid;
none;
submit data
78.133 C2 H6 O S C(CS)...
DLL A:1441;
B:1438;
Valid;
Valid;
none;
none;
submit data
465.354 C18 H20 N5 O8 P c1ccc...
K A:1440;
B:1446;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
MG A:1439;
B:1445;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
PEG B:1439;
B:1440;
B:1441;
B:1442;
B:1443;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Y4O 1.9 Å EC: 6.2.1.30 CRYSTAL STRUCTURE OF PAAK2 IN COMPLEX WITH PHENYLACETYL ADEN BURKHOLDERIA CENOCEPACIA LIGASE PHENYLACETIC ACID DEGRADATION PATHWAY
Ref.: DEFINING A STRUCTURAL AND KINETIC RATIONALE FOR PARALOGOUS COPIES OF PHENYLACETATE-COA LIGASES FROM THE CYSTIC FIBROSIS PATHOGEN BURKHOLDERIA CENOCEPACIA J2315. J.BIOL.CHEM. V. 286 15577 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2Y4O - DLL C18 H20 N5 O8 P c1ccc(cc1)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Y4N - DLL C18 H20 N5 O8 P c1ccc(cc1)....
2 2Y27 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 2Y4O - DLL C18 H20 N5 O8 P c1ccc(cc1)....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Y4N - DLL C18 H20 N5 O8 P c1ccc(cc1)....
2 2Y27 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 2Y4O - DLL C18 H20 N5 O8 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DLL; Similar ligands found: 352
No: Ligand ECFP6 Tc MDL keys Tc
1 DLL 1 1
2 OOB 0.736264 1
3 CA0 0.729412 0.958904
4 FA5 0.729167 0.972603
5 KG4 0.72093 0.958904
6 5AL 0.719101 0.972222
7 8LQ 0.706522 0.945946
8 SRP 0.703297 0.945946
9 8LH 0.703297 0.945946
10 8LE 0.7 0.933333
11 A2D 0.690476 0.958333
12 FYA 0.680412 0.918919
13 3UK 0.677083 0.986111
14 BA3 0.674419 0.958333
15 B5V 0.670103 0.972603
16 WAQ 0.670103 0.921053
17 B4P 0.666667 0.958333
18 AP5 0.666667 0.958333
19 ADP 0.666667 0.931507
20 1ZZ 0.663265 0.875
21 8QN 0.663158 0.972222
22 AT4 0.659091 0.894737
23 AN2 0.659091 0.918919
24 4AD 0.65625 0.933333
25 AMO 0.65625 0.945946
26 PAJ 0.65625 0.897436
27 AR6 0.655556 0.958333
28 APR 0.655556 0.958333
29 AMP 0.654762 0.930556
30 A 0.654762 0.930556
31 M33 0.651685 0.918919
32 ADX 0.651685 0.839506
33 00A 0.649485 0.946667
34 NB8 0.646465 0.909091
35 HEJ 0.644444 0.931507
36 50T 0.644444 0.893333
37 ATP 0.644444 0.931507
38 ACP 0.644444 0.906667
39 YAP 0.643564 0.959459
40 PRX 0.637363 0.881579
41 5FA 0.637363 0.931507
42 AQP 0.637363 0.931507
43 LAD 0.636364 0.897436
44 ANP 0.634409 0.906667
45 9SN 0.633663 0.934211
46 AHX 0.632653 0.884615
47 ABM 0.632184 0.905405
48 45A 0.632184 0.905405
49 SAP 0.630435 0.883117
50 AD9 0.630435 0.906667
51 AGS 0.630435 0.883117
52 ME8 0.63 0.875
53 PTJ 0.63 0.909091
54 TXA 0.63 0.945946
55 B5M 0.627451 0.959459
56 B5Y 0.627451 0.959459
57 OAD 0.626263 0.958904
58 PR8 0.62 0.886076
59 AP2 0.617977 0.894737
60 A12 0.617977 0.894737
61 GAP 0.617021 0.932432
62 ACQ 0.617021 0.906667
63 AU1 0.615385 0.906667
64 OZV 0.612245 0.931507
65 SRA 0.609195 0.881579
66 LAQ 0.607477 0.875
67 TYM 0.605505 0.972603
68 SON 0.604396 0.945946
69 ATF 0.604167 0.894737
70 4UV 0.6 0.959459
71 3OD 0.598039 0.958904
72 6YZ 0.597938 0.906667
73 ADV 0.595745 0.92
74 RBY 0.595745 0.92
75 HQG 0.591837 0.945205
76 IOT 0.589286 0.843373
77 YLP 0.587156 0.853659
78 ADP MG 0.586957 0.930556
79 A22 0.585859 0.945205
80 APC 0.585106 0.894737
81 T99 0.583333 0.894737
82 TAT 0.583333 0.894737
83 9ZA 0.58 0.921053
84 25A 0.58 0.958333
85 5SV 0.58 0.8375
86 9ZD 0.58 0.921053
87 9X8 0.578431 0.907895
88 XAH 0.575472 0.851852
89 A1R 0.574257 0.871795
90 A3R 0.574257 0.871795
91 ADQ 0.574257 0.958904
92 4UU 0.574074 0.959459
93 YLC 0.571429 0.875
94 YLB 0.571429 0.853659
95 DAL AMP 0.57 0.945205
96 DQV 0.568807 0.972222
97 NXX 0.567568 0.972603
98 DND 0.567568 0.972603
99 4UW 0.567568 0.922078
100 BT5 0.564103 0.843373
101 ATP MG 0.5625 0.930556
102 APC MG 0.5625 0.905405
103 ADP PO3 0.5625 0.930556
104 YLA 0.556522 0.853659
105 MAP 0.554455 0.883117
106 BIS 0.552381 0.871795
107 AYB 0.551724 0.843373
108 MYR AMP 0.54717 0.851852
109 25L 0.54717 0.945205
110 LMS 0.544444 0.817073
111 TYR AMP 0.541284 0.933333
112 AMP DBH 0.541284 0.906667
113 ALF ADP 0.54 0.858974
114 ADP ALF 0.54 0.858974
115 NAX 0.539823 0.886076
116 CNA 0.538462 0.945946
117 G3A 0.536364 0.909091
118 OMR 0.535088 0.864198
119 TXE 0.535088 0.921053
120 VO4 ADP 0.534653 0.918919
121 ADP VO4 0.534653 0.918919
122 M24 0.532787 0.910256
123 AOC 0.532609 0.810811
124 G5P 0.531532 0.909091
125 GA7 0.531532 0.894737
126 AFH 0.531532 0.897436
127 48N 0.530973 0.909091
128 A5D 0.530612 0.8
129 NAD 0.529412 0.972222
130 TXD 0.526316 0.921053
131 5AS 0.526316 0.770115
132 NAI 0.526316 0.921053
133 6V0 0.526316 0.909091
134 G5A 0.525253 0.790698
135 8PZ 0.522936 0.811765
136 F2R 0.521008 0.853659
137 A3D 0.520661 0.958904
138 YLY 0.520325 0.843373
139 N0B 0.52 0.876543
140 SSA 0.519608 0.790698
141 ARG AMP 0.517857 0.841463
142 A3P 0.515789 0.930556
143 PAP 0.515152 0.917808
144 A A 0.514019 0.931507
145 GTA 0.513274 0.875
146 DZD 0.512397 0.897436
147 ADN 0.511905 0.808219
148 RAB 0.511905 0.808219
149 XYA 0.511905 0.808219
150 5CD 0.511628 0.794521
151 A5A 0.509804 0.819277
152 TSB 0.509615 0.809524
153 5CA 0.509615 0.790698
154 ADP BMA 0.504673 0.932432
155 YSA 0.504505 0.811765
156 7MD 0.504425 0.875
157 LPA AMP 0.504348 0.851852
158 AP0 0.504274 0.884615
159 T5A 0.504202 0.853659
160 COD 0.504132 0.802326
161 PPS 0.5 0.817073
162 A4P 0.5 0.833333
163 5N5 0.5 0.783784
164 3AM 0.5 0.890411
165 VMS 0.5 0.8
166 52H 0.5 0.790698
167 54H 0.5 0.8
168 UP5 0.5 0.933333
169 TAD 0.5 0.873418
170 ZID 0.496063 0.958904
171 649 0.495726 0.775281
172 ATP A A A 0.495495 0.944444
173 ATP A 0.495495 0.944444
174 JB6 0.495413 0.896104
175 8X1 0.495238 0.764045
176 53H 0.495238 0.790698
177 A4D 0.494253 0.783784
178 NAE 0.492063 0.933333
179 AMP NAD 0.491803 0.972222
180 139 0.491667 0.886076
181 UPA 0.491525 0.921053
182 4TC 0.491525 0.909091
183 B1U 0.491071 0.766667
184 2A5 0.49 0.857143
185 6RE 0.489362 0.728395
186 3DH 0.48913 0.763158
187 DTA 0.488889 0.8
188 P5A 0.486239 0.755556
189 LSS 0.485981 0.772727
190 NSS 0.485981 0.790698
191 DSZ 0.485981 0.811765
192 A2R 0.485714 0.945205
193 ATR 0.485149 0.90411
194 ITT 0.484848 0.878378
195 80F 0.483871 0.876543
196 WSA 0.483051 0.821429
197 AHZ 0.482759 0.851852
198 9K8 0.481818 0.764045
199 NVA LMS 0.481481 0.764045
200 H1Q 0.48 0.891892
201 BTX 0.479675 0.831325
202 ADJ 0.479339 0.864198
203 J7C 0.479167 0.7375
204 7MC 0.478992 0.853659
205 KOY 0.478632 0.864865
206 7D5 0.478261 0.842105
207 AR6 AR6 0.478261 0.958333
208 EP4 0.477778 0.74359
209 LEU LMS 0.477064 0.764045
210 NAQ 0.476562 0.909091
211 7D3 0.474227 0.844156
212 4YB 0.474138 0.813953
213 GSU 0.472727 0.811765
214 KAA 0.472727 0.764045
215 M2T 0.472527 0.725
216 AF3 ADP 3PG 0.470588 0.873418
217 7D4 0.47 0.844156
218 A2P 0.469388 0.916667
219 MTA 0.467391 0.763158
220 EAD 0.465649 0.886076
221 5X8 0.465347 0.8
222 A3N 0.463918 0.753247
223 V3L 0.461538 0.958333
224 GJV 0.459184 0.719512
225 6MZ 0.459184 0.891892
226 6AD 0.457143 0.85
227 NAJ PZO 0.456693 0.884615
228 NDC 0.455882 0.909091
229 NEC 0.453608 0.736842
230 A3G 0.453608 0.789474
231 JSQ 0.451923 0.883117
232 HFD 0.451923 0.883117
233 P1H 0.451852 0.864198
234 NDE 0.451852 0.945946
235 SFG 0.45098 0.786667
236 NA7 0.45045 0.894737
237 IMO 0.44898 0.890411
238 ZAS 0.447917 0.75641
239 F2N 0.446667 0.804598
240 J4G 0.446429 0.933333
241 A3S 0.445545 0.8
242 FB0 0.445255 0.775281
243 G A A A 0.444444 0.884615
244 NO7 0.444444 0.87013
245 A G 0.444444 0.896104
246 0WD 0.444444 0.909091
247 S4M 0.444444 0.659091
248 SA8 0.442308 0.740741
249 2AM 0.442105 0.878378
250 ARU 0.441441 0.804878
251 MHZ 0.441176 0.689655
252 U A G G 0.440945 0.896104
253 MAO 0.44 0.75
254 FAQ 0.439716 0.795455
255 LQJ 0.439655 0.931507
256 2SA 0.439252 0.92
257 DSH 0.438776 0.716049
258 SAI 0.438095 0.769231
259 SAH 0.438095 0.779221
260 A A A 0.4375 0.893333
261 A6D 0.4375 0.73494
262 DAT 0.436893 0.844156
263 NJP 0.436508 0.933333
264 AVV 0.436364 0.860759
265 GEK 0.436364 0.772152
266 SMM 0.435185 0.717647
267 S7M 0.435185 0.722892
268 3AT 0.433962 0.905405
269 DTP 0.433962 0.844156
270 SAM 0.433962 0.722892
271 4TA 0.433071 0.841463
272 0UM 0.432432 0.731707
273 7C5 0.432203 0.855263
274 NAJ PYZ 0.431818 0.841463
275 A7D 0.431373 0.766234
276 8Q2 0.430894 0.784091
277 DCA 0.430769 0.793103
278 N5A 0.43 0.727273
279 EEM 0.429907 0.722892
280 AAT 0.429907 0.698795
281 N6P 0.428571 0.902778
282 OVE 0.428571 0.844156
283 D3Y 0.427273 0.802632
284 GGZ 0.427273 0.792683
285 AV2 0.425926 0.855263
286 6C6 0.424528 0.846154
287 N5O 0.424242 0.753247
288 V1N 0.423729 0.958333
289 6K6 0.423423 0.891892
290 A3T 0.423077 0.810811
291 NHD 0.421875 0.945205
292 3NZ 0.421053 0.794872
293 NPW 0.420635 0.875
294 6IA 0.420561 0.804878
295 5AD 0.420455 0.736111
296 9JJ 0.42 0.875
297 ETB 0.419847 0.802326
298 OZP 0.418033 0.78481
299 NAP 0.41791 0.958904
300 FNK 0.417808 0.795455
301 AMZ 0.416667 0.878378
302 C2R 0.416667 0.891892
303 FA9 0.415584 0.853659
304 NVA 2AD 0.415094 0.75
305 TAP 0.414815 0.896104
306 Z5A 0.414815 0.811765
307 ODP 0.414062 0.897436
308 KB1 0.413793 0.753086
309 0T1 0.413534 0.793103
310 COA 0.413534 0.793103
311 SLU 0.412214 0.802326
312 U A 0.412214 0.921053
313 NA0 0.411765 0.945946
314 71V 0.411765 0.848101
315 DA 0.41 0.842105
316 D5M 0.41 0.842105
317 SFD 0.409722 0.744681
318 2VA 0.409524 0.789474
319 NDP 0.409449 0.909091
320 FDA 0.408451 0.823529
321 TXP 0.40625 0.909091
322 NZQ 0.40625 0.897436
323 FAI 0.405941 0.878378
324 AAM 0.405941 0.930556
325 6FA 0.405594 0.853659
326 SXZ 0.405172 0.743902
327 APU 0.404762 0.907895
328 CAO 0.404412 0.766667
329 AMX 0.404412 0.802326
330 30N 0.404412 0.726316
331 COS 0.404412 0.775281
332 SCD 0.404255 0.813953
333 7DD 0.403846 0.917808
334 BV8 0.403509 0.788889
335 62X 0.403509 0.697674
336 CA8 0.402778 0.721649
337 KGA 0.402778 0.736842
338 BYC 0.402778 0.795455
339 Y3J 0.402174 0.716216
340 N01 0.401515 0.945205
341 CMX 0.40146 0.813953
342 SCO 0.40146 0.813953
343 PGS 0.4 0.825
344 FAD 0.4 0.864198
345 N37 0.4 0.792208
346 7D7 0.4 0.733333
347 FAS 0.4 0.864198
348 K15 0.4 0.714286
349 KGP 0.4 0.704082
350 PO4 PO4 A A A A PO4 0.4 0.916667
351 YZS 0.4 0.704082
352 101 0.4 0.842105
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Y4O; Ligand: DLL; 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: 2y4o.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2Y4O; Ligand: DLL; 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: 2y4o.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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