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 (2D)
Ligand no: 1; Ligand: DLL; Similar ligands found: 375
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 8LH 0.703297 0.945946
9 SRP 0.703297 0.945946
10 8LE 0.7 0.933333
11 A2D 0.690476 0.958333
12 QA7 0.688172 0.933333
13 FYA 0.680412 0.918919
14 3UK 0.677083 0.986111
15 BA3 0.674419 0.958333
16 WAQ 0.670103 0.921053
17 B5V 0.670103 0.972603
18 AP5 0.666667 0.958333
19 B4P 0.666667 0.958333
20 ADP 0.666667 0.931507
21 1ZZ 0.663265 0.875
22 8QN 0.663158 0.972222
23 AT4 0.659091 0.894737
24 AN2 0.659091 0.918919
25 PAJ 0.65625 0.897436
26 4AD 0.65625 0.933333
27 AMO 0.65625 0.945946
28 APR 0.655556 0.958333
29 AR6 0.655556 0.958333
30 A 0.654762 0.930556
31 AMP 0.654762 0.930556
32 M33 0.651685 0.918919
33 ADX 0.651685 0.839506
34 00A 0.649485 0.946667
35 NB8 0.646465 0.909091
36 ATP 0.644444 0.931507
37 ACP 0.644444 0.906667
38 50T 0.644444 0.893333
39 HEJ 0.644444 0.931507
40 5FA 0.637363 0.931507
41 AQP 0.637363 0.931507
42 PRX 0.637363 0.881579
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 45A 0.632184 0.905405
48 ABM 0.632184 0.905405
49 AGS 0.630435 0.883117
50 AD9 0.630435 0.906667
51 ME8 0.63 0.875
52 TXA 0.63 0.945946
53 PTJ 0.63 0.909091
54 AMP MG 0.627907 0.916667
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 A12 0.617977 0.894737
60 AP2 0.617977 0.894737
61 ACQ 0.617021 0.906667
62 GAP 0.617021 0.932432
63 AU1 0.615385 0.906667
64 OZV 0.612245 0.931507
65 V2G 0.610526 0.909091
66 SRA 0.609195 0.881579
67 LAQ 0.607477 0.875
68 TYM 0.605505 0.972603
69 SON 0.604396 0.945946
70 ATF 0.604167 0.894737
71 4UV 0.6 0.959459
72 3OD 0.598039 0.958904
73 6YZ 0.597938 0.906667
74 RBY 0.595745 0.92
75 ADV 0.595745 0.92
76 HQG 0.591837 0.945205
77 IOT 0.589286 0.843373
78 YLP 0.587156 0.853659
79 ADP MG 0.586957 0.930556
80 ADP BEF 0.586957 0.930556
81 A22 0.585859 0.945205
82 APC 0.585106 0.894737
83 JNT 0.584158 0.906667
84 T99 0.583333 0.894737
85 TAT 0.583333 0.894737
86 25A 0.58 0.958333
87 9ZA 0.58 0.921053
88 9ZD 0.58 0.921053
89 5SV 0.58 0.8375
90 9X8 0.578431 0.907895
91 XAH 0.575472 0.851852
92 ADQ 0.574257 0.958904
93 A3R 0.574257 0.871795
94 A1R 0.574257 0.871795
95 4UU 0.574074 0.959459
96 YLC 0.571429 0.875
97 YLB 0.571429 0.853659
98 DAL AMP 0.57 0.945205
99 DQV 0.568807 0.972222
100 DND 0.567568 0.972603
101 4UW 0.567568 0.922078
102 BT5 0.564103 0.843373
103 APC MG 0.5625 0.905405
104 ADP PO3 0.5625 0.930556
105 ATP MG 0.5625 0.930556
106 BEF ADP 0.556701 0.905405
107 YLA 0.556522 0.853659
108 ANP MG 0.555556 0.918919
109 MAP 0.554455 0.883117
110 BIS 0.552381 0.871795
111 AYB 0.551724 0.843373
112 MYR AMP 0.54717 0.851852
113 25L 0.54717 0.945205
114 LMS 0.544444 0.817073
115 AMP DBH 0.541284 0.906667
116 ALF ADP 0.54 0.858974
117 VO4 ADP 0.54 0.906667
118 NAX 0.539823 0.886076
119 CNA 0.538462 0.945946
120 KMQ 0.537037 0.92
121 G3A 0.536364 0.909091
122 OMR 0.535088 0.864198
123 TXE 0.535088 0.921053
124 M24 0.532787 0.910256
125 AOC 0.532609 0.810811
126 AFH 0.531532 0.897436
127 GA7 0.531532 0.894737
128 G5P 0.531532 0.909091
129 48N 0.530973 0.909091
130 A5D 0.530612 0.8
131 NAD 0.529412 0.972222
132 NAI 0.526316 0.921053
133 6V0 0.526316 0.909091
134 5AS 0.526316 0.770115
135 TXD 0.526316 0.921053
136 G5A 0.525253 0.790698
137 8PZ 0.522936 0.811765
138 F2R 0.521008 0.853659
139 A3D 0.520661 0.958904
140 YLY 0.520325 0.843373
141 N0B 0.52 0.876543
142 SSA 0.519608 0.790698
143 ARG AMP 0.517857 0.841463
144 L3W 0.517241 0.92
145 D4F 0.516129 0.898734
146 A3P 0.515789 0.930556
147 PAP 0.515152 0.917808
148 GTA 0.513274 0.875
149 DZD 0.512397 0.897436
150 XYA 0.511905 0.808219
151 ADN 0.511905 0.808219
152 RAB 0.511905 0.808219
153 5CD 0.511628 0.794521
154 A5A 0.509804 0.819277
155 TSB 0.509615 0.809524
156 5CA 0.509615 0.790698
157 ADP BMA 0.504673 0.932432
158 YSA 0.504505 0.811765
159 7MD 0.504425 0.875
160 LPA AMP 0.504348 0.851852
161 NAD TDB 0.504274 0.958333
162 AP0 0.504274 0.884615
163 NAD IBO 0.504274 0.958333
164 T5A 0.504202 0.853659
165 COD 0.504132 0.802326
166 UP5 0.5 0.933333
167 3AM 0.5 0.890411
168 PPS 0.5 0.817073
169 52H 0.5 0.790698
170 TAD 0.5 0.873418
171 54H 0.5 0.8
172 VMS 0.5 0.8
173 5N5 0.5 0.783784
174 A4P 0.5 0.833333
175 ZID 0.496063 0.958904
176 649 0.495726 0.775281
177 ATP A A A 0.495495 0.944444
178 ATP A 0.495495 0.944444
179 JB6 0.495413 0.896104
180 53H 0.495238 0.790698
181 8X1 0.495238 0.764045
182 A4D 0.494253 0.783784
183 NAE 0.492063 0.933333
184 AMP NAD 0.491803 0.972222
185 139 0.491667 0.886076
186 UPA 0.491525 0.921053
187 4TC 0.491525 0.909091
188 B1U 0.491071 0.766667
189 QXP 0.490566 0.776471
190 2A5 0.49 0.857143
191 6RE 0.489362 0.728395
192 3DH 0.48913 0.763158
193 DTA 0.488889 0.8
194 P5A 0.486239 0.755556
195 LSS 0.485981 0.772727
196 DSZ 0.485981 0.811765
197 NSS 0.485981 0.790698
198 A2R 0.485714 0.945205
199 ATR 0.485149 0.90411
200 ITT 0.484848 0.878378
201 80F 0.483871 0.876543
202 WSA 0.483051 0.821429
203 AHZ 0.482759 0.851852
204 9K8 0.481818 0.764045
205 NVA LMS 0.481481 0.764045
206 H1Q 0.48 0.891892
207 BTX 0.479675 0.831325
208 ADJ 0.479339 0.864198
209 J7C 0.479167 0.7375
210 7MC 0.478992 0.853659
211 KOY 0.478632 0.864865
212 AR6 AR6 0.478261 0.958333
213 7D5 0.478261 0.842105
214 EP4 0.477778 0.74359
215 NAQ 0.476562 0.909091
216 7D3 0.474227 0.844156
217 4YB 0.474138 0.813953
218 KAA 0.472727 0.764045
219 GSU 0.472727 0.811765
220 M2T 0.472527 0.725
221 AF3 ADP 3PG 0.470588 0.873418
222 ALF ADP 3PG 0.470588 0.873418
223 7D4 0.47 0.844156
224 A2P 0.469388 0.916667
225 MTA 0.467391 0.763158
226 EAD 0.465649 0.886076
227 5X8 0.465347 0.8
228 A3N 0.463918 0.753247
229 QXG 0.463636 0.767442
230 LEU LMS 0.463636 0.761364
231 V3L 0.461538 0.958333
232 NWW 0.460674 0.75
233 R2V 0.459459 0.776471
234 6MZ 0.459184 0.891892
235 GJV 0.459184 0.719512
236 6AD 0.457143 0.85
237 NAJ PZO 0.456693 0.884615
238 NDC 0.455882 0.909091
239 A3G 0.453608 0.789474
240 NEC 0.453608 0.736842
241 O02 0.451923 0.860759
242 HFD 0.451923 0.883117
243 JSQ 0.451923 0.883117
244 P1H 0.451852 0.864198
245 NDE 0.451852 0.945946
246 SFG 0.45098 0.786667
247 NA7 0.45045 0.894737
248 IMO 0.44898 0.890411
249 V47 0.448598 0.847222
250 ZAS 0.447917 0.75641
251 F2N 0.446667 0.804598
252 J4G 0.446429 0.933333
253 A3S 0.445545 0.8
254 FB0 0.445255 0.775281
255 S4M 0.444444 0.659091
256 NO7 0.444444 0.87013
257 0WD 0.444444 0.909091
258 K3K 0.443478 0.792208
259 SA8 0.442308 0.740741
260 2AM 0.442105 0.878378
261 ARU 0.441441 0.804878
262 MHZ 0.441176 0.689655
263 MAO 0.44 0.75
264 FAQ 0.439716 0.795455
265 LQJ 0.439655 0.931507
266 38V 0.439394 0.875
267 2SA 0.439252 0.92
268 DSH 0.438776 0.716049
269 SAI 0.438095 0.769231
270 SAH 0.438095 0.779221
271 A6D 0.4375 0.73494
272 CUU 0.436893 0.905405
273 DAT 0.436893 0.844156
274 NJP 0.436508 0.933333
275 GEK 0.436364 0.772152
276 AVV 0.436364 0.860759
277 K3E 0.435897 0.782051
278 S7M 0.435185 0.722892
279 SMM 0.435185 0.717647
280 SAM 0.433962 0.722892
281 3AT 0.433962 0.905405
282 DTP 0.433962 0.844156
283 4TA 0.433071 0.841463
284 0UM 0.432432 0.731707
285 7C5 0.432203 0.855263
286 NAJ PYZ 0.431818 0.841463
287 A7D 0.431373 0.766234
288 8Q2 0.430894 0.784091
289 DCA 0.430769 0.793103
290 N5A 0.43 0.727273
291 AAT 0.429907 0.698795
292 EEM 0.429907 0.722892
293 K2R 0.429825 0.918919
294 FAJ 0.428571 0.843373
295 OVE 0.428571 0.844156
296 N6P 0.428571 0.902778
297 GGZ 0.427273 0.792683
298 D3Y 0.427273 0.802632
299 NWQ 0.427083 0.72973
300 AV2 0.425926 0.855263
301 KXW 0.425 0.7625
302 6C6 0.424528 0.846154
303 N5O 0.424242 0.753247
304 V1N 0.423729 0.958333
305 NAD BBN 0.423611 0.853659
306 6K6 0.423423 0.891892
307 A3T 0.423077 0.810811
308 NHD 0.421875 0.945205
309 3NZ 0.421053 0.794872
310 NPW 0.420635 0.875
311 6IA 0.420561 0.804878
312 5AD 0.420455 0.736111
313 9JJ 0.42 0.875
314 ETB 0.419847 0.802326
315 OZP 0.418033 0.78481
316 NAP 0.41791 0.958904
317 NAD CJ3 0.417808 0.823529
318 FNK 0.417808 0.795455
319 C2R 0.416667 0.891892
320 AMZ 0.416667 0.878378
321 FA9 0.415584 0.853659
322 K2W 0.415254 0.731707
323 NVA 2AD 0.415094 0.75
324 TAP 0.414815 0.896104
325 Z5A 0.414815 0.811765
326 EU9 0.414634 0.735632
327 ODP 0.414062 0.897436
328 KY5 0.413793 0.7375
329 KB1 0.413793 0.753086
330 COA 0.413534 0.793103
331 0T1 0.413534 0.793103
332 SLU 0.412214 0.802326
333 NA0 0.411765 0.945946
334 71V 0.411765 0.848101
335 DA 0.41 0.842105
336 D5M 0.41 0.842105
337 SFD 0.409722 0.744681
338 2VA 0.409524 0.789474
339 Q2V 0.409449 0.753086
340 NDP 0.409449 0.909091
341 FDA 0.408451 0.823529
342 NZQ 0.40625 0.897436
343 TXP 0.40625 0.909091
344 FAI 0.405941 0.878378
345 AAM 0.405941 0.930556
346 6FA 0.405594 0.853659
347 SXZ 0.405172 0.743902
348 APU 0.404762 0.907895
349 CAO 0.404412 0.766667
350 30N 0.404412 0.726316
351 AMX 0.404412 0.802326
352 COS 0.404412 0.775281
353 SCD 0.404255 0.813953
354 7DD 0.403846 0.917808
355 BV8 0.403509 0.788889
356 62X 0.403509 0.697674
357 CA8 0.402778 0.721649
358 KGA 0.402778 0.736842
359 BYC 0.402778 0.795455
360 Y3J 0.402174 0.716216
361 KY2 0.401786 0.702381
362 N01 0.401515 0.945205
363 SCO 0.40146 0.813953
364 CMX 0.40146 0.813953
365 PGS 0.4 0.825
366 7D7 0.4 0.733333
367 FAS 0.4 0.864198
368 FAD 0.4 0.864198
369 PO4 PO4 A A A A PO4 0.4 0.916667
370 Q2P 0.4 0.72619
371 N37 0.4 0.792208
372 101 0.4 0.842105
373 KGP 0.4 0.704082
374 YZS 0.4 0.704082
375 K15 0.4 0.714286
Similar Ligands (3D)
Ligand no: 1; Ligand: DLL; Similar ligands found: 0
No: Ligand Similarity coefficient
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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