Receptor
PDB id Resolution Class Description Source Keywords
2Y4N 1.92 Å EC: 6.2.1.30 PAAK1 IN COMPLEX WITH PHENYLACETYL ADENYLATE BURKHOLDERIA CENOCEPACIA LIGASE PHENYLACETIC ACID DEGRADATION PATHWAY
Ref.: DEFINING A STRUCTURAL AND KINETIC RATIONALE FOR PAR COPIES OF PHENYLACETATE-COA LIGASES FROM THE CYSTIC 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 A:1435;
B:1435;
B:1436;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
78.133 C2 H6 O S C(CS)...
DLL A:1436;
D:1437;
Valid;
Valid;
none;
none;
submit data
465.354 C18 H20 N5 O8 P c1ccc...
MG A:1432;
A:1433;
B:1431;
B:1432;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PAC B:1433;
Valid;
none;
submit data
136.148 C8 H8 O2 c1ccc...
PEG A:1434;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
PGE B:1434;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Y4N 1.92 Å EC: 6.2.1.30 PAAK1 IN COMPLEX WITH PHENYLACETYL ADENYLATE BURKHOLDERIA CENOCEPACIA LIGASE PHENYLACETIC ACID DEGRADATION PATHWAY
Ref.: DEFINING A STRUCTURAL AND KINETIC RATIONALE FOR PAR COPIES OF PHENYLACETATE-COA LIGASES FROM THE CYSTIC PATHOGEN BURKHOLDERIA CENOCEPACIA J2315. J.BIOL.CHEM. V. 286 15577 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2Y4N - DLL C18 H20 N5 O8 P c1ccc(cc1)....
2 2Y27 - ATP C10 H16 N5 O13 P3 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 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: 311
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 5AL 0.719101 0.972222
6 SRP 0.703297 0.945946
7 A2D 0.690476 0.958333
8 FYA 0.680412 0.918919
9 3UK 0.677083 0.986111
10 BA3 0.674419 0.958333
11 WAQ 0.670103 0.921053
12 B4P 0.666667 0.958333
13 ADP 0.666667 0.931507
14 AP5 0.666667 0.958333
15 1ZZ 0.663265 0.875
16 8QN 0.663158 0.972222
17 AN2 0.659091 0.918919
18 PAJ 0.65625 0.897436
19 AMO 0.65625 0.945946
20 4AD 0.65625 0.933333
21 APR 0.655556 0.958333
22 AR6 0.655556 0.958333
23 A 0.654762 0.930556
24 AMP 0.654762 0.930556
25 ADX 0.651685 0.839506
26 M33 0.651685 0.918919
27 00A 0.649485 0.946667
28 NB8 0.646465 0.909091
29 50T 0.644444 0.893333
30 ACP 0.644444 0.906667
31 ATP 0.644444 0.931507
32 YAP 0.643564 0.959459
33 PRX 0.637363 0.881579
34 5FA 0.637363 0.931507
35 AQP 0.637363 0.931507
36 LAD 0.636364 0.897436
37 ANP 0.634409 0.906667
38 9SN 0.633663 0.934211
39 AHX 0.632653 0.884615
40 ABM 0.632184 0.905405
41 SAP 0.630435 0.883117
42 AD9 0.630435 0.906667
43 AGS 0.630435 0.883117
44 TXA 0.63 0.945946
45 PTJ 0.63 0.909091
46 ME8 0.63 0.875
47 OAD 0.626263 0.958904
48 AMP MG 0.62069 0.88
49 PR8 0.62 0.886076
50 AP2 0.617977 0.894737
51 A12 0.617977 0.894737
52 GAP 0.617021 0.932432
53 ACQ 0.617021 0.906667
54 AU1 0.615385 0.906667
55 SRA 0.609195 0.881579
56 LAQ 0.607477 0.875
57 TYM 0.605505 0.972603
58 SON 0.604396 0.945946
59 ATF 0.604167 0.894737
60 4UV 0.6 0.959459
61 3OD 0.598039 0.958904
62 ADV 0.595745 0.92
63 RBY 0.595745 0.92
64 IOT 0.589286 0.843373
65 YLP 0.587156 0.853659
66 A22 0.585859 0.945205
67 APC 0.585106 0.894737
68 TAT 0.583333 0.894737
69 ADP MG 0.580645 0.893333
70 25A 0.58 0.958333
71 5SV 0.58 0.8375
72 XAH 0.575472 0.851852
73 ADP BEF 0.574468 0.87013
74 BEF ADP 0.574468 0.87013
75 ADQ 0.574257 0.958904
76 A1R 0.574257 0.871795
77 4UU 0.574074 0.959459
78 YLC 0.571429 0.875
79 YLB 0.571429 0.853659
80 DAL AMP 0.57 0.945205
81 4UW 0.567568 0.922078
82 DND 0.567568 0.972603
83 NXX 0.567568 0.972603
84 BT5 0.564103 0.843373
85 ADP PO3 0.5625 0.930556
86 ATP MG 0.556701 0.893333
87 YLA 0.556522 0.853659
88 MAP 0.554455 0.883117
89 BIS 0.552381 0.871795
90 AYB 0.551724 0.843373
91 ANP MG 0.55 0.883117
92 MYR AMP 0.54717 0.851852
93 25L 0.54717 0.945205
94 TYR AMP 0.546296 0.945946
95 AMP DBH 0.541284 0.906667
96 ADP ALF 0.54 0.858974
97 ALF ADP 0.54 0.858974
98 NAX 0.539823 0.886076
99 CNA 0.538462 0.945946
100 G3A 0.536364 0.909091
101 OMR 0.535088 0.864198
102 TXE 0.535088 0.921053
103 VO4 ADP 0.534653 0.918919
104 ADP VO4 0.534653 0.918919
105 M24 0.532787 0.910256
106 AOC 0.532609 0.810811
107 G5P 0.531532 0.909091
108 AFH 0.531532 0.897436
109 48N 0.530973 0.909091
110 A5D 0.530612 0.8
111 NAD 0.529412 0.972222
112 6V0 0.526316 0.909091
113 NAI 0.526316 0.921053
114 5AS 0.526316 0.770115
115 TXD 0.526316 0.921053
116 G5A 0.525253 0.790698
117 A3D 0.520661 0.958904
118 YLY 0.520325 0.843373
119 N0B 0.52 0.876543
120 SSA 0.519608 0.790698
121 A3P 0.515789 0.930556
122 PAP 0.515152 0.917808
123 A A 0.514019 0.931507
124 GTA 0.513274 0.875
125 DZD 0.512397 0.897436
126 ADN 0.511905 0.808219
127 RAB 0.511905 0.808219
128 XYA 0.511905 0.808219
129 5CD 0.511628 0.794521
130 A5A 0.509804 0.819277
131 5CA 0.509615 0.790698
132 TSB 0.509615 0.809524
133 ARG AMP 0.508772 0.841463
134 ADP BMA 0.504673 0.932432
135 YSA 0.504505 0.811765
136 7MD 0.504425 0.875
137 LPA AMP 0.504348 0.851852
138 AP0 0.504274 0.884615
139 T5A 0.504202 0.853659
140 COD 0.504132 0.802326
141 3AM 0.5 0.890411
142 VMS 0.5 0.8
143 PPS 0.5 0.817073
144 TAD 0.5 0.873418
145 54H 0.5 0.8
146 52H 0.5 0.790698
147 5N5 0.5 0.783784
148 UP5 0.5 0.933333
149 A4P 0.5 0.833333
150 ZID 0.496063 0.958904
151 649 0.495726 0.775281
152 ATP A A A 0.495495 0.944444
153 JB6 0.495413 0.896104
154 53H 0.495238 0.790698
155 A4D 0.494253 0.783784
156 NAE 0.492063 0.933333
157 139 0.491667 0.886076
158 UPA 0.491525 0.921053
159 4TC 0.491525 0.909091
160 2A5 0.49 0.857143
161 6RE 0.489362 0.728395
162 3DH 0.48913 0.763158
163 DTA 0.488889 0.8
164 P5A 0.486239 0.755556
165 DSZ 0.485981 0.811765
166 NSS 0.485981 0.790698
167 LSS 0.485981 0.772727
168 A2R 0.485714 0.945205
169 ATR 0.485149 0.90411
170 ITT 0.484848 0.878378
171 NAD IBO 0.483607 0.907895
172 WSA 0.483051 0.821429
173 AHZ 0.482759 0.851852
174 NVA LMS 0.481481 0.772727
175 BTX 0.479675 0.831325
176 ADJ 0.479339 0.864198
177 J7C 0.479167 0.7375
178 7MC 0.478992 0.853659
179 7D5 0.478261 0.842105
180 AR6 AR6 0.478261 0.958333
181 EP4 0.477778 0.74359
182 LEU LMS 0.477064 0.772727
183 NAQ 0.476562 0.909091
184 7D3 0.474227 0.844156
185 4YB 0.474138 0.813953
186 GSU 0.472727 0.811765
187 KAA 0.472727 0.764045
188 M2T 0.472527 0.725
189 AF3 ADP 3PG 0.470588 0.873418
190 ALF ADP 3PG 0.470588 0.873418
191 LA8 ALF 3PG 0.470588 0.873418
192 7D4 0.47 0.844156
193 A2P 0.469388 0.916667
194 MTA 0.467391 0.763158
195 EAD 0.465649 0.886076
196 5X8 0.465347 0.8
197 NAJ PYZ 0.465116 0.886076
198 A3N 0.463918 0.753247
199 AMP NAD 0.461538 0.945946
200 V3L 0.461538 0.958333
201 GJV 0.459184 0.719512
202 6AD 0.457143 0.85
203 NAJ PZO 0.456693 0.884615
204 NDC 0.455882 0.909091
205 A3G 0.453608 0.789474
206 NEC 0.453608 0.736842
207 P1H 0.451852 0.864198
208 NDE 0.451852 0.945946
209 SFG 0.45098 0.786667
210 NA7 0.45045 0.894737
211 IMO 0.44898 0.890411
212 ZAS 0.447917 0.75641
213 F2N 0.446667 0.804598
214 A3S 0.445545 0.8
215 FB0 0.445255 0.775281
216 0WD 0.444444 0.909091
217 G A A A 0.444444 0.884615
218 S4M 0.444444 0.659091
219 SA8 0.442308 0.740741
220 2AM 0.442105 0.878378
221 ARU 0.441441 0.804878
222 MHZ 0.441176 0.689655
223 U A G G 0.440945 0.896104
224 MAO 0.44 0.75
225 FAQ 0.439716 0.795455
226 2SA 0.439252 0.92
227 DSH 0.438776 0.716049
228 SAI 0.438095 0.769231
229 SAH 0.438095 0.779221
230 A A A 0.4375 0.893333
231 A6D 0.4375 0.73494
232 DAT 0.436893 0.844156
233 NJP 0.436508 0.933333
234 AVV 0.436364 0.860759
235 GEK 0.436364 0.772152
236 SMM 0.435185 0.717647
237 S7M 0.435185 0.722892
238 SAM 0.433962 0.722892
239 3AT 0.433962 0.905405
240 DTP 0.433962 0.844156
241 4TA 0.433071 0.841463
242 0UM 0.432432 0.731707
243 7C5 0.432203 0.855263
244 A7D 0.431373 0.766234
245 DCA 0.430769 0.793103
246 EEM 0.429907 0.722892
247 AAT 0.429907 0.698795
248 N6P 0.428571 0.902778
249 OVE 0.428571 0.844156
250 D3Y 0.427273 0.802632
251 GGZ 0.427273 0.792683
252 AV2 0.425926 0.855263
253 6C6 0.424528 0.846154
254 V1N 0.423729 0.958333
255 NAD BBN 0.423611 0.853659
256 6K6 0.423423 0.891892
257 A3T 0.423077 0.810811
258 NHD 0.421875 0.945205
259 3NZ 0.421053 0.794872
260 NPW 0.420635 0.875
261 6IA 0.420561 0.804878
262 5AD 0.420455 0.736111
263 ETB 0.419847 0.802326
264 NAP 0.41791 0.958904
265 NAD CJ3 0.417808 0.823529
266 FNK 0.417808 0.795455
267 AMZ 0.416667 0.878378
268 C2R 0.416667 0.891892
269 FA9 0.415584 0.853659
270 Z5A 0.414815 0.811765
271 TAP 0.414815 0.896104
272 ODP 0.414062 0.897436
273 KB1 0.413793 0.753086
274 0T1 0.413534 0.793103
275 COA 0.413534 0.793103
276 SLU 0.412214 0.802326
277 71V 0.411765 0.848101
278 NA0 0.411765 0.945946
279 D5M 0.41 0.842105
280 DA 0.41 0.842105
281 SFD 0.409722 0.744681
282 2VA 0.409524 0.789474
283 NDP 0.409449 0.909091
284 FDA 0.408451 0.823529
285 TXP 0.40625 0.909091
286 NZQ 0.40625 0.897436
287 AAM 0.405941 0.930556
288 FAI 0.405941 0.878378
289 6FA 0.405594 0.853659
290 SXZ 0.405172 0.743902
291 APU 0.404762 0.907895
292 AMX 0.404412 0.802326
293 30N 0.404412 0.726316
294 COS 0.404412 0.775281
295 CAO 0.404412 0.766667
296 SCD 0.404255 0.813953
297 7DD 0.403846 0.917808
298 62X 0.403509 0.697674
299 CA8 0.402778 0.721649
300 BYC 0.402778 0.795455
301 Y3J 0.402174 0.716216
302 N01 0.401515 0.945205
303 CMX 0.40146 0.813953
304 SCO 0.40146 0.813953
305 7D7 0.4 0.733333
306 101 0.4 0.842105
307 FAD 0.4 0.864198
308 PO4 PO4 A A A A PO4 0.4 0.916667
309 PGS 0.4 0.825
310 K15 0.4 0.714286
311 FAS 0.4 0.864198
Ligand no: 2; Ligand: PAC; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 PAC 1 1
2 PPY 0.612903 0.666667
3 4HP 0.5 0.684211
4 HCI 0.5 0.8
5 CLT 0.485714 0.705882
6 3HP 0.459459 0.65
7 LNW 0.45 0.619048
8 5PV 0.447368 0.666667
9 HF2 0.432432 0.684211
10 HFA 0.432432 0.684211
11 BZS 0.425 0.684211
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Y4N; Ligand: PAC; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 2y4n.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3NYQ AMP 0.00003113 0.51643 1.60183
2 3NYQ MCA 0.00002861 0.51643 1.60183
3 1ZX5 LFR 0.02519 0.40531 1.66667
4 5C5H 4YB 0.000181 0.47328 2.51716
5 5MSD AMP 0.00000008244 0.56858 2.746
6 5MSD BEZ 0.0000003584 0.56858 2.746
7 2CFC KPC 0.004107 0.44714 2.8
8 5MST AMP 0.000000284 0.59463 2.97483
9 5MST FUM 0.000001025 0.52784 2.97483
10 5HM3 649 0.00002576 0.44316 3.20366
11 2J5V RGP 0.02092 0.41285 3.54223
12 1AMU AMP 0.00000041 0.60298 3.89016
13 3KL3 GCU 0.03791 0.40333 3.99003
14 4DG8 AMP 0.0000653 0.46032 4.11899
15 5IE3 AMP 0.00001466 0.52384 5.03433
16 5IE3 OXD 0.00001466 0.52384 5.03433
17 4B2G V1N 0.00526 0.40256 5.49199
18 5KOD AMP 0.001313 0.40683 5.72082
19 3E7W AMP 0.0002611 0.48106 6.17849
20 4GR5 APC 0.000009586 0.54768 6.40732
21 1V25 ANP 0.0000222 0.42666 6.63616
22 2BDG PBZ 0.02234 0.41178 6.72646
23 4R0M FA5 0.00001544 0.51905 7.09382
24 5EY9 5SV 0.00002858 0.46636 8.92449
25 4GXQ ATP 0.000001194 0.55448 9.38215
26 4FUT ATP 0.000001918 0.55211 9.38215
27 3DHV DAL AMP 0.000002653 0.54003 9.38215
28 1MDB AMP DBH 0.000002049 0.53797 9.83982
29 2PKA BEN 0.02286 0.40938 10
30 5D6J ATP 0.0001077 0.46289 10.0687
31 3KXW 1ZZ 0.0000005829 0.57997 10.7551
32 4D57 ARG AMP 0.000001547 0.45886 11.6705
33 5BSR COA 0.00003569 0.53945 12.5858
34 5BSR AMP 0.00002308 0.53363 12.5858
35 1RY2 AMP 0.00000199 0.51063 13.2723
36 4OXI GAP 0.000006524 0.52375 15.103
37 5OE4 3UK 0.00005054 0.48669 15.2334
38 2D1S SLU 0.000001055 0.57526 16.7048
39 5N9X ATP 0.0000006411 0.56574 17.6201
40 5N9X 8QN 0.0000116 0.51572 17.6201
41 3CW9 AMP 0.00001867 0.52155 18.7643
42 3IES M24 0.000007556 0.54509 19.4508
43 3O84 HTJ 0.00004709 0.45932 19.6796
44 5X8G S0N 0.0002029 0.49856 24.4851
Pocket No.: 2; Query (leader) PDB : 2Y4N; Ligand: DLL; Similar sites found: 64
This union binding pocket(no: 2) in the query (biounit: 2y4n.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3NYQ AMP 0.000009048 0.50638 1.60183
2 3NYQ MCA 0.000008399 0.50593 1.60183
3 2NNJ 225 0.007082 0.43796 1.60183
4 3NKS ACJ 0.01358 0.40796 1.60183
5 1ZX5 LFR 0.03229 0.40869 1.66667
6 4CJN QNZ 0.01435 0.42995 1.83066
7 2XVL PXN 0.04063 0.40267 2.0595
8 5C5H 4YB 0.00003144 0.47132 2.51716
9 3LKF PC 0.006758 0.42871 2.67559
10 5MSD BEZ 0.000000009374 0.55791 2.746
11 5MSD AMP 0.00000001105 0.53109 2.746
12 2CFC KPC 0.01513 0.42782 2.8
13 5MST AMP 0.00000005436 0.6443 2.97483
14 5MST FUM 0.0000003706 0.57405 2.97483
15 2IVD ACJ 0.01193 0.41797 2.97483
16 5HM3 649 0.00001141 0.48899 3.20366
17 1GPM AMP 0.02961 0.40263 3.43249
18 1AMU AMP 0.000001521 0.5934 3.89016
19 2X1L ADN 0.0267 0.40424 3.89016
20 1HQL GLA MBG 0.0277 0.40541 3.89105
21 4E28 9MZ 0.0365 0.40494 4
22 4DG8 AMP 0.00006517 0.42121 4.11899
23 5TE1 7A2 0.03419 0.40246 4.80549
24 5IE3 AMP 0.0000009198 0.53707 5.03433
25 5IE3 OXD 0.0000009198 0.53707 5.03433
26 2XG5 EC2 0.009628 0.43157 5.04587
27 2XG5 EC5 0.009628 0.43157 5.04587
28 1W0O SIA 0.009351 0.4388 5.72082
29 1I9Z 2IP 0.02785 0.40858 5.76369
30 3E7W AMP 0.0001125 0.51144 6.17849
31 4GR5 APC 0.00001852 0.54901 6.40732
32 4EPM AMP 0.00546 0.40664 6.40732
33 3OBT SLB 0.01141 0.42236 6.45161
34 1V25 ANP 0.000006846 0.47418 6.63616
35 4FGC PQ0 0.04544 0.40137 6.66667
36 4R0M FA5 0.0000002077 0.55083 7.09382
37 3LL5 IP8 0.03045 0.41239 7.63052
38 5EY9 5SV 0.000008371 0.51396 8.92449
39 1H8P PC 0.01325 0.41739 9.17431
40 2JFV FLC 0.04782 0.40241 9.27835
41 3DHV DAL AMP 0.0000001304 0.61246 9.38215
42 4GXQ ATP 0.000002328 0.55837 9.38215
43 4FUT ATP 0.000003427 0.55711 9.38215
44 1MDB AMP DBH 0.00000006003 0.53113 9.83982
45 5D6J ATP 0.00002948 0.43925 10.0687
46 3KXW 1ZZ 0.0000005087 0.53598 10.7551
47 1LOB MMA 0.02316 0.4113 11.5385
48 4D57 ARG AMP 0.0000002196 0.51935 11.6705
49 5BSR COA 0.000003816 0.54924 12.5858
50 5BSR AMP 0.000002426 0.54123 12.5858
51 1RY2 AMP 0.0000001336 0.49795 13.2723
52 4OXI GAP 0.0000002011 0.52113 15.103
53 5OE4 3UK 0.000001863 0.56255 15.2334
54 2D1S SLU 0.0000002302 0.56213 16.7048
55 5N9X 8QN 0.00000009092 0.54228 17.6201
56 5N9X ATP 0.0000005031 0.51111 17.6201
57 3CW9 AMP 0.000002233 0.57848 18.7643
58 3CW9 01A 0.004247 0.40008 18.7643
59 3IES M24 0.0000008689 0.54766 19.4508
60 3O84 HTJ 0.00000688 0.51738 19.6796
61 5X8G S0N 0.00002223 0.51114 24.4851
62 4RLQ 3SK 0.00006656 0.41842 25.4005
63 1PG4 PRX 0.000004152 0.43603 28.3753
64 1PG4 COA 0.000004152 0.43603 28.3753
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