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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: 326
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 B5V 0.670103 0.972603
12 WAQ 0.670103 0.921053
13 AP5 0.666667 0.958333
14 ADP 0.666667 0.931507
15 B4P 0.666667 0.958333
16 1ZZ 0.663265 0.875
17 8QN 0.663158 0.972222
18 AT4 0.659091 0.894737
19 AN2 0.659091 0.918919
20 AMO 0.65625 0.945946
21 PAJ 0.65625 0.897436
22 4AD 0.65625 0.933333
23 AR6 0.655556 0.958333
24 APR 0.655556 0.958333
25 A 0.654762 0.930556
26 AMP 0.654762 0.930556
27 M33 0.651685 0.918919
28 ADX 0.651685 0.839506
29 00A 0.649485 0.946667
30 NB8 0.646465 0.909091
31 50T 0.644444 0.893333
32 ACP 0.644444 0.906667
33 ATP 0.644444 0.931507
34 HEJ 0.644444 0.931507
35 YAP 0.643564 0.959459
36 PRX 0.637363 0.881579
37 AQP 0.637363 0.931507
38 5FA 0.637363 0.931507
39 LAD 0.636364 0.897436
40 ANP 0.634409 0.906667
41 9SN 0.633663 0.934211
42 AHX 0.632653 0.884615
43 ABM 0.632184 0.905405
44 AD9 0.630435 0.906667
45 AGS 0.630435 0.883117
46 SAP 0.630435 0.883117
47 ME8 0.63 0.875
48 PTJ 0.63 0.909091
49 TXA 0.63 0.945946
50 B5M 0.627451 0.959459
51 B5Y 0.627451 0.959459
52 OAD 0.626263 0.958904
53 PR8 0.62 0.886076
54 AP2 0.617977 0.894737
55 A12 0.617977 0.894737
56 GAP 0.617021 0.932432
57 ACQ 0.617021 0.906667
58 AU1 0.615385 0.906667
59 SRA 0.609195 0.881579
60 LAQ 0.607477 0.875
61 TYM 0.605505 0.972603
62 SON 0.604396 0.945946
63 ATF 0.604167 0.894737
64 4UV 0.6 0.959459
65 3OD 0.598039 0.958904
66 6YZ 0.597938 0.906667
67 RBY 0.595745 0.92
68 ADV 0.595745 0.92
69 IOT 0.589286 0.843373
70 YLP 0.587156 0.853659
71 A22 0.585859 0.945205
72 APC 0.585106 0.894737
73 TAT 0.583333 0.894737
74 T99 0.583333 0.894737
75 9ZA 0.58 0.921053
76 9ZD 0.58 0.921053
77 5SV 0.58 0.8375
78 25A 0.58 0.958333
79 9X8 0.578431 0.907895
80 XAH 0.575472 0.851852
81 ADQ 0.574257 0.958904
82 A3R 0.574257 0.871795
83 A1R 0.574257 0.871795
84 4UU 0.574074 0.959459
85 YLB 0.571429 0.853659
86 YLC 0.571429 0.875
87 DAL AMP 0.57 0.945205
88 DQV 0.568807 0.972222
89 NXX 0.567568 0.972603
90 DND 0.567568 0.972603
91 4UW 0.567568 0.922078
92 BT5 0.564103 0.843373
93 ADP PO3 0.5625 0.930556
94 YLA 0.556522 0.853659
95 MAP 0.554455 0.883117
96 BIS 0.552381 0.871795
97 AYB 0.551724 0.843373
98 25L 0.54717 0.945205
99 MYR AMP 0.54717 0.851852
100 LMS 0.544444 0.817073
101 TYR AMP 0.541284 0.933333
102 AMP DBH 0.541284 0.906667
103 ALF ADP 0.54 0.858974
104 ADP ALF 0.54 0.858974
105 NAX 0.539823 0.886076
106 CNA 0.538462 0.945946
107 G3A 0.536364 0.909091
108 TXE 0.535088 0.921053
109 OMR 0.535088 0.864198
110 ADP VO4 0.534653 0.918919
111 VO4 ADP 0.534653 0.918919
112 M24 0.532787 0.910256
113 AOC 0.532609 0.810811
114 AFH 0.531532 0.897436
115 G5P 0.531532 0.909091
116 GA7 0.531532 0.894737
117 48N 0.530973 0.909091
118 A5D 0.530612 0.8
119 NAD 0.529412 0.972222
120 6V0 0.526316 0.909091
121 TXD 0.526316 0.921053
122 5AS 0.526316 0.770115
123 NAI 0.526316 0.921053
124 G5A 0.525253 0.790698
125 8PZ 0.522936 0.811765
126 F2R 0.521008 0.853659
127 A3D 0.520661 0.958904
128 YLY 0.520325 0.843373
129 N0B 0.52 0.876543
130 SSA 0.519608 0.790698
131 ARG AMP 0.517857 0.841463
132 A3P 0.515789 0.930556
133 PAP 0.515152 0.917808
134 A A 0.514019 0.931507
135 GTA 0.513274 0.875
136 DZD 0.512397 0.897436
137 ADN 0.511905 0.808219
138 RAB 0.511905 0.808219
139 XYA 0.511905 0.808219
140 5CD 0.511628 0.794521
141 A5A 0.509804 0.819277
142 5CA 0.509615 0.790698
143 TSB 0.509615 0.809524
144 ADP BMA 0.504673 0.932432
145 YSA 0.504505 0.811765
146 7MD 0.504425 0.875
147 LPA AMP 0.504348 0.851852
148 AP0 0.504274 0.884615
149 T5A 0.504202 0.853659
150 COD 0.504132 0.802326
151 A4P 0.5 0.833333
152 PPS 0.5 0.817073
153 UP5 0.5 0.933333
154 5N5 0.5 0.783784
155 3AM 0.5 0.890411
156 VMS 0.5 0.8
157 54H 0.5 0.8
158 TAD 0.5 0.873418
159 52H 0.5 0.790698
160 ZID 0.496063 0.958904
161 649 0.495726 0.775281
162 ATP A A A 0.495495 0.944444
163 JB6 0.495413 0.896104
164 8X1 0.495238 0.764045
165 53H 0.495238 0.790698
166 A4D 0.494253 0.783784
167 NAE 0.492063 0.933333
168 AMP NAD 0.491803 0.972222
169 139 0.491667 0.886076
170 4TC 0.491525 0.909091
171 UPA 0.491525 0.921053
172 2A5 0.49 0.857143
173 6RE 0.489362 0.728395
174 3DH 0.48913 0.763158
175 DTA 0.488889 0.8
176 P5A 0.486239 0.755556
177 NSS 0.485981 0.790698
178 DSZ 0.485981 0.811765
179 LSS 0.485981 0.772727
180 A2R 0.485714 0.945205
181 ATR 0.485149 0.90411
182 ITT 0.484848 0.878378
183 80F 0.483871 0.876543
184 WSA 0.483051 0.821429
185 AHZ 0.482759 0.851852
186 9K8 0.481818 0.764045
187 NVA LMS 0.481481 0.764045
188 BTX 0.479675 0.831325
189 ADJ 0.479339 0.864198
190 J7C 0.479167 0.7375
191 7MC 0.478992 0.853659
192 AR6 AR6 0.478261 0.958333
193 7D5 0.478261 0.842105
194 EP4 0.477778 0.74359
195 LEU LMS 0.477064 0.764045
196 NAQ 0.476562 0.909091
197 7D3 0.474227 0.844156
198 4YB 0.474138 0.813953
199 GSU 0.472727 0.811765
200 KAA 0.472727 0.764045
201 M2T 0.472527 0.725
202 AF3 ADP 3PG 0.470588 0.873418
203 7D4 0.47 0.844156
204 A2P 0.469388 0.916667
205 MTA 0.467391 0.763158
206 EAD 0.465649 0.886076
207 5X8 0.465347 0.8
208 A3N 0.463918 0.753247
209 V3L 0.461538 0.958333
210 GJV 0.459184 0.719512
211 6AD 0.457143 0.85
212 NAJ PZO 0.456693 0.884615
213 NDC 0.455882 0.909091
214 A3G 0.453608 0.789474
215 NEC 0.453608 0.736842
216 HFD 0.451923 0.883117
217 P1H 0.451852 0.864198
218 NDE 0.451852 0.945946
219 SFG 0.45098 0.786667
220 NA7 0.45045 0.894737
221 IMO 0.44898 0.890411
222 ZAS 0.447917 0.75641
223 F2N 0.446667 0.804598
224 A3S 0.445545 0.8
225 FB0 0.445255 0.775281
226 S4M 0.444444 0.659091
227 0WD 0.444444 0.909091
228 A G 0.444444 0.896104
229 G A A A 0.444444 0.884615
230 SA8 0.442308 0.740741
231 2AM 0.442105 0.878378
232 ARU 0.441441 0.804878
233 MHZ 0.441176 0.689655
234 U A G G 0.440945 0.896104
235 MAO 0.44 0.75
236 FAQ 0.439716 0.795455
237 2SA 0.439252 0.92
238 DSH 0.438776 0.716049
239 SAI 0.438095 0.769231
240 SAH 0.438095 0.779221
241 A6D 0.4375 0.73494
242 A A A 0.4375 0.893333
243 DAT 0.436893 0.844156
244 NJP 0.436508 0.933333
245 GEK 0.436364 0.772152
246 AVV 0.436364 0.860759
247 S7M 0.435185 0.722892
248 SMM 0.435185 0.717647
249 SAM 0.433962 0.722892
250 3AT 0.433962 0.905405
251 DTP 0.433962 0.844156
252 4TA 0.433071 0.841463
253 0UM 0.432432 0.731707
254 7C5 0.432203 0.855263
255 NAJ PYZ 0.431818 0.841463
256 A7D 0.431373 0.766234
257 8Q2 0.430894 0.784091
258 DCA 0.430769 0.793103
259 AAT 0.429907 0.698795
260 EEM 0.429907 0.722892
261 N6P 0.428571 0.902778
262 OVE 0.428571 0.844156
263 D3Y 0.427273 0.802632
264 GGZ 0.427273 0.792683
265 AV2 0.425926 0.855263
266 6C6 0.424528 0.846154
267 V1N 0.423729 0.958333
268 6K6 0.423423 0.891892
269 A3T 0.423077 0.810811
270 NHD 0.421875 0.945205
271 3NZ 0.421053 0.794872
272 NPW 0.420635 0.875
273 6IA 0.420561 0.804878
274 5AD 0.420455 0.736111
275 9JJ 0.42 0.875
276 ETB 0.419847 0.802326
277 NAP 0.41791 0.958904
278 FNK 0.417808 0.795455
279 AMZ 0.416667 0.878378
280 C2R 0.416667 0.891892
281 FA9 0.415584 0.853659
282 NVA 2AD 0.415094 0.75
283 Z5A 0.414815 0.811765
284 TAP 0.414815 0.896104
285 ODP 0.414062 0.897436
286 KB1 0.413793 0.753086
287 0T1 0.413534 0.793103
288 COA 0.413534 0.793103
289 U A 0.412214 0.921053
290 SLU 0.412214 0.802326
291 NA0 0.411765 0.945946
292 71V 0.411765 0.848101
293 DA 0.41 0.842105
294 D5M 0.41 0.842105
295 SFD 0.409722 0.744681
296 2VA 0.409524 0.789474
297 NDP 0.409449 0.909091
298 FDA 0.408451 0.823529
299 TXP 0.40625 0.909091
300 NZQ 0.40625 0.897436
301 AAM 0.405941 0.930556
302 FAI 0.405941 0.878378
303 6FA 0.405594 0.853659
304 SXZ 0.405172 0.743902
305 APU 0.404762 0.907895
306 AMX 0.404412 0.802326
307 COS 0.404412 0.775281
308 CAO 0.404412 0.766667
309 30N 0.404412 0.726316
310 SCD 0.404255 0.813953
311 7DD 0.403846 0.917808
312 62X 0.403509 0.697674
313 BV8 0.403509 0.788889
314 CA8 0.402778 0.721649
315 BYC 0.402778 0.795455
316 Y3J 0.402174 0.716216
317 N01 0.401515 0.945205
318 CMX 0.40146 0.813953
319 SCO 0.40146 0.813953
320 PO4 PO4 A A A A PO4 0.4 0.916667
321 FAS 0.4 0.864198
322 FAD 0.4 0.864198
323 101 0.4 0.842105
324 7D7 0.4 0.733333
325 K15 0.4 0.714286
326 PGS 0.4 0.825
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: 113
This union binding pocket(no: 1) in the query (biounit: 2y4o.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4OFJ HIS 1.12867
2 2NNJ 225 1.58014
3 5W5R PYR 1.67464
4 4B2G V1N 2.25734
5 4XWM CBI 2.34949
6 2XCU C5P 2.40642
7 4D57 ARG AMP 2.48307
8 2FMD MAN MAN 2.5
9 1MVQ MMA 2.54237
10 3ITA AIC 2.55682
11 5MSD BEZ 2.7088
12 5MSD AMP 2.7088
13 4CJN QNZ 2.7088
14 6GN6 MAL 2.7088
15 2QPU QPU 2.71605
16 2QPU QPS 2.71605
17 4NYT PC 2.76498
18 3LTW HLZ 2.85714
19 2BQP GLC 2.99145
20 2EB5 OXL 2.99625
21 1V6A TRE 3.01205
22 3G2Y GF4 3.04183
23 5KOD AMP 3.16027
24 6E1Q CFA 3.16027
25 2VAR AMP 3.19489
26 1HSL HIS 3.36134
27 4XJ7 ADE 3.37079
28 1V25 ANP 3.386
29 4DG8 AMP 3.386
30 2Z3U CRR 3.52941
31 3NYQ AMP 3.56436
32 3NYQ MCA 3.56436
33 5A9A UTP 3.7037
34 5C5H 4YB 3.75276
35 6FGL UO1 3.80952
36 5TE1 7A2 3.83747
37 2XHK AKG 4.05405
38 4RLQ 3SK 4.06321
39 1AX2 NDG GAL 4.1841
40 2BVE PH5 4.20168
41 4DS0 A2G GAL NAG FUC 4.29448
42 1MJT ITU 4.32277
43 4GXQ ATP 4.51467
44 4FUT ATP 4.51467
45 2XQ0 BES 4.74041
46 2D2F ADP 4.8
47 2UWN SCR 4.81283
48 5FPE 3TR 4.90956
49 1WOG 16D 4.91803
50 2IVD ACJ 4.96614
51 1GPM AMP 4.96614
52 2X1L ADN 5.19187
53 1DQN IMU 5.21739
54 5VKM GAL SIA 5.24691
55 3F5A SIA GAL NAG 5.28455
56 4FGC PQ0 5.45455
57 1W0O SIA 5.64334
58 5OWC AYZ 5.7377
59 2V57 PRL 5.78947
60 2Q89 6CS 5.83658
61 3E7W AMP 6.09481
62 1JI0 ATP 6.25
63 3CF6 SP1 6.58683
64 6AA8 NAD 6.62252
65 2BDG PBZ 6.72646
66 1MDB AMP DBH 6.99774
67 4R0M FA5 6.99844
68 1XF1 CIT 7.22348
69 6B74 BEN 7.40741
70 5TCI MLI 7.6087
71 4FK7 P34 7.86026
72 1F9V ADP 8.06916
73 2XG5 EC5 8.09249
74 2XG5 EC2 8.09249
75 1H8P PC 8.25688
76 1LNX URI 8.64198
77 3KXW 1ZZ 8.80361
78 1LOB MMA 8.83978
79 3KCC CMP 10
80 1AMU AMP 10.6095
81 5IE3 OXD 10.6095
82 5IE3 AMP 10.6095
83 5WHT SIA GAL GLC 10.8696
84 5OE4 3UK 11.5479
85 5D6J ATP 12.1896
86 4RHS SIA SIA GAL 12.2951
87 5HM3 649 12.6411
88 5N81 8Q2 12.6464
89 4GR5 APC 12.8668
90 5EY9 5SV 12.8668
91 5MST AMP 13.3183
92 5MST FUM 13.3183
93 4OXI GAP 14.2212
94 3IES M24 14.2212
95 3O84 HTJ 15.1242
96 5N9X 8QN 16.7043
97 5N9X ATP 16.7043
98 5N9X THR 16.7043
99 1RY2 AMP 17.833
100 3CW9 AMP 18.0587
101 3CW9 01A 18.0587
102 2D1S SLU 19.1874
103 3C5E ATP 19.4131
104 1OFS SUC 22.9167
105 5X8G S0N 23.4763
106 5WM2 SAL 24.1535
107 5WM2 AMP 24.1535
108 2V7B BEZ 31.1512
109 3DHV DAL AMP 31.6027
110 5BSR COA 33.1828
111 5BSR AMP 33.1828
112 1PG4 COA 34.3115
113 1PG4 PRX 34.3115
Pocket No.: 2; Query (leader) PDB : 2Y4O; Ligand: DLL; Similar sites found with APoc: 18
This union binding pocket(no: 2) in the query (biounit: 2y4o.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 6EGU 43Y 1.3544
3 3LKF PC 1.67224
4 4TR9 38D 3.25203
5 5OSW DIU 3.386
6 5V6F MAN BMA MAN 3.62319
7 1LES GLC FRU 3.8674
8 3UEC ALA ARG TPO LYS 4.10959
9 3O5N BR0 4.46429
10 3CB2 GDP 4.51467
11 2D3Y DU 5.02283
12 2W68 SIA GAL BGC 5.64103
13 5F6U 5VK 5.73248
14 5D85 FLC 6.44172
15 3VV5 SLZ 6.53846
16 2QJY UQ2 6.95187
17 2D3N GLC GLC GLC 7.67494
18 4K30 NLG 13.125
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