Receptor
PDB id Resolution Class Description Source Keywords
4ZJZ 1.7 Å EC: 6.-.-.- CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH BENZO RHODOPSEUDOMONAS PALUSTRIS SUBSTRATE SPECIFICITY KINETICS LIGASE
Ref.: KINETICALLY AND CRYSTALLOGRAPHICALLY GUIDED MUTATIO BENZOATE COA LIGASE (BADA) ELUCIDATE MECHANISM AND SUBSTRATE PERMISSIVITY. BIOCHEMISTRY V. 54 6230 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BEZ B:601;
A:1001;
Valid;
Valid;
none;
none;
submit data
122.121 C7 H6 O2 c1ccc...
GOL B:606;
A:1005;
B:602;
A:1002;
B:604;
B:608;
A:1004;
B:607;
B:605;
A:1003;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
OOB B:603;
A:1000;
Valid;
Valid;
none;
none;
submit data
451.327 C17 H18 N5 O8 P c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RLQ 1.63 Å EC: 6.-.-.- CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH O-TOL RHODOPSEUDOMONAS PALUSTRIS SUBSTRATE SPECIFICITY KINETICS LIGASE
Ref.: KINETICALLY AND CRYSTALLOGRAPHICALLY GUIDED MUTATIO BENZOATE COA LIGASE (BADA) ELUCIDATE MECHANISM AND SUBSTRATE PERMISSIVITY. BIOCHEMISTRY V. 54 6230 2015
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4RLQ - 3SK C8 H8 O2 Cc1ccccc1C....
2 4RM2 - 3U4 C7 H5 F O2 c1ccc(c(c1....
3 4RMN - C21 C5 H4 O2 S c1cc(sc1)C....
4 4RM3 - FOA C5 H4 O3 c1cc(oc1)C....
5 4RLF - 4MA C8 H8 O2 Cc1ccc(cc1....
6 4ZJZ - OOB C17 H18 N5 O8 P c1ccc(cc1)....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4RLQ - 3SK C8 H8 O2 Cc1ccccc1C....
2 4RM2 - 3U4 C7 H5 F O2 c1ccc(c(c1....
3 4RMN - C21 C5 H4 O2 S c1cc(sc1)C....
4 4RM3 - FOA C5 H4 O3 c1cc(oc1)C....
5 4RLF - 4MA C8 H8 O2 Cc1ccc(cc1....
6 4ZJZ - OOB C17 H18 N5 O8 P c1ccc(cc1)....
7 2V7B - BEZ C7 H6 O2 c1ccc(cc1)....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4RLQ - 3SK C8 H8 O2 Cc1ccccc1C....
2 4RM2 - 3U4 C7 H5 F O2 c1ccc(c(c1....
3 4RMN - C21 C5 H4 O2 S c1cc(sc1)C....
4 4RM3 - FOA C5 H4 O3 c1cc(oc1)C....
5 4RLF - 4MA C8 H8 O2 Cc1ccc(cc1....
6 4ZJZ - OOB C17 H18 N5 O8 P c1ccc(cc1)....
7 2V7B - BEZ C7 H6 O2 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BEZ; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 BEZ 1 1
2 8OZ 0.517241 0.625
3 1Y6 0.464286 0.666667
4 NIO 0.433333 0.625
5 PHB 0.428571 0.625
6 PHT 0.423077 0.625
7 3HB 0.419355 0.625
8 Z82 0.413793 0.666667
9 MBO 0.413793 0.769231
10 174 0.413793 0.666667
11 4MA 0.413793 0.909091
12 3BZ 0.40625 0.666667
Ligand no: 2; Ligand: OOB; Similar ligands found: 316
No: Ligand ECFP6 Tc MDL keys Tc
1 OOB 1 1
2 00A 0.816092 0.946667
3 3UK 0.747253 0.986111
4 CA0 0.746988 0.958904
5 DLL 0.736264 1
6 A2D 0.707317 0.958333
7 9SN 0.697917 0.934211
8 5AL 0.696629 0.972222
9 FA5 0.690722 0.972603
10 BA3 0.690476 0.958333
11 AP5 0.682353 0.958333
12 B4P 0.682353 0.958333
13 ADP 0.682353 0.931507
14 SRP 0.681319 0.945946
15 AN2 0.674419 0.918919
16 A 0.670732 0.930556
17 AMP 0.670732 0.930556
18 M33 0.666667 0.918919
19 WAQ 0.666667 0.921053
20 ADX 0.666667 0.839506
21 AD9 0.662921 0.906667
22 1ZZ 0.659794 0.875
23 8QN 0.659574 0.972222
24 ATP 0.659091 0.931507
25 50T 0.659091 0.893333
26 ACP 0.659091 0.906667
27 AMO 0.652632 0.945946
28 4AD 0.652632 0.933333
29 PAJ 0.652632 0.897436
30 AQP 0.651685 0.931507
31 APR 0.651685 0.958333
32 5FA 0.651685 0.931507
33 PRX 0.651685 0.881579
34 AR6 0.651685 0.958333
35 ABM 0.647059 0.905405
36 AGS 0.644444 0.883117
37 SAP 0.644444 0.883117
38 FYA 0.642857 0.918919
39 TXA 0.642857 0.945946
40 M24 0.637168 0.910256
41 AMP MG 0.635294 0.88
42 PR8 0.632653 0.886076
43 LAD 0.632653 0.897436
44 AP2 0.632184 0.894737
45 A12 0.632184 0.894737
46 ANP 0.630435 0.906667
47 ACQ 0.630435 0.906667
48 NB8 0.626263 0.909091
49 PTJ 0.626263 0.909091
50 ME8 0.626263 0.875
51 YAP 0.623762 0.959459
52 SRA 0.623529 0.881579
53 OAD 0.622449 0.958904
54 ATF 0.617021 0.894737
55 GAP 0.612903 0.932432
56 AHX 0.612245 0.884615
57 4UV 0.61165 0.959459
58 AU1 0.611111 0.906667
59 3OD 0.61 0.958904
60 LAQ 0.603774 0.875
61 ADQ 0.602041 0.958904
62 TYM 0.601852 0.972603
63 SON 0.6 0.945946
64 DAL AMP 0.597938 0.945205
65 A22 0.597938 0.945205
66 APC 0.597826 0.894737
67 TAT 0.595745 0.894737
68 ADP MG 0.593407 0.893333
69 DND 0.592593 0.972603
70 NXX 0.592593 0.972603
71 5SV 0.591837 0.8375
72 25A 0.591837 0.958333
73 ADV 0.591398 0.92
74 RBY 0.591398 0.92
75 ADP BEF 0.586957 0.87013
76 BEF ADP 0.586957 0.87013
77 A1R 0.585859 0.871795
78 4UU 0.584906 0.959459
79 ADP PO3 0.574468 0.930556
80 XAH 0.571429 0.851852
81 IOT 0.571429 0.843373
82 YLP 0.568807 0.853659
83 ATP MG 0.568421 0.893333
84 4UW 0.563636 0.922078
85 BIS 0.563107 0.871795
86 AOC 0.561798 0.810811
87 CNA 0.561404 0.945946
88 25L 0.557692 0.945205
89 MYR AMP 0.557692 0.851852
90 YLB 0.553571 0.853659
91 YLC 0.553571 0.875
92 YLA 0.552632 0.853659
93 NAD 0.551724 0.972222
94 ADP ALF 0.55102 0.858974
95 ALF ADP 0.55102 0.858974
96 MAP 0.55 0.883117
97 NAX 0.54955 0.886076
98 BT5 0.547009 0.843373
99 DZD 0.547009 0.897436
100 G3A 0.546296 0.909091
101 ADP VO4 0.545455 0.918919
102 VO4 ADP 0.545455 0.918919
103 ANP MG 0.545455 0.883117
104 TXE 0.544643 0.921053
105 OMR 0.544643 0.864198
106 A3D 0.542373 0.958904
107 TYR AMP 0.542056 0.945946
108 G5P 0.541284 0.909091
109 48N 0.540541 0.909091
110 AMP DBH 0.537037 0.906667
111 TXD 0.535714 0.921053
112 6V0 0.535714 0.909091
113 NAI 0.535714 0.921053
114 AYB 0.534483 0.843373
115 ADP BMA 0.528846 0.932432
116 AFH 0.527273 0.897436
117 A3P 0.526882 0.930556
118 PAP 0.525773 0.917808
119 ADN 0.52439 0.808219
120 XYA 0.52439 0.808219
121 RAB 0.52439 0.808219
122 A A 0.52381 0.931507
123 5CD 0.52381 0.794521
124 GTA 0.522523 0.875
125 5AS 0.521277 0.770115
126 G5A 0.520408 0.790698
127 SSA 0.514852 0.790698
128 LPA AMP 0.513274 0.851852
129 T5A 0.512821 0.853659
130 5N5 0.511905 0.783784
131 3AM 0.511111 0.890411
132 A5D 0.510204 0.8
133 PPS 0.51 0.817073
134 TAD 0.508929 0.873418
135 UP5 0.508772 0.933333
136 A4D 0.505882 0.783784
137 A5A 0.504951 0.819277
138 TSB 0.504854 0.809524
139 JB6 0.504673 0.896104
140 ATP A A A 0.504587 0.944444
141 ARG AMP 0.504425 0.841463
142 NAD IBO 0.504202 0.907895
143 YLY 0.504065 0.843373
144 AMP NAD 0.504 0.945946
145 ZID 0.504 0.958904
146 N0B 0.504 0.876543
147 UPA 0.5 0.921053
148 COD 0.5 0.802326
149 AP0 0.5 0.884615
150 2A5 0.5 0.857143
151 DTA 0.5 0.8
152 4TC 0.5 0.909091
153 7MD 0.5 0.875
154 NAQ 0.496 0.909091
155 A4P 0.495726 0.833333
156 VMS 0.495146 0.8
157 54H 0.495146 0.8
158 52H 0.495146 0.790698
159 ATR 0.494949 0.90411
160 AHZ 0.491228 0.851852
161 5CA 0.490385 0.790698
162 53H 0.490385 0.790698
163 7D5 0.488889 0.842105
164 EP4 0.488636 0.74359
165 NAE 0.488 0.933333
166 139 0.487395 0.886076
167 ADJ 0.487395 0.864198
168 AR6 AR6 0.486726 0.958333
169 EAD 0.484375 0.886076
170 7D3 0.484211 0.844156
171 NAJ PYZ 0.484127 0.886076
172 6RE 0.483871 0.728395
173 3DH 0.483516 0.763158
174 M2T 0.483146 0.725
175 P5A 0.481481 0.755556
176 NSS 0.481132 0.790698
177 DSZ 0.481132 0.811765
178 LSS 0.481132 0.772727
179 A2R 0.480769 0.945205
180 6AD 0.480392 0.85
181 7D4 0.479592 0.844156
182 ITT 0.479592 0.878378
183 A2P 0.479167 0.916667
184 ALF ADP 3PG 0.478632 0.873418
185 LA8 ALF 3PG 0.478632 0.873418
186 AF3 ADP 3PG 0.478632 0.873418
187 649 0.478632 0.775281
188 MTA 0.477778 0.763158
189 NVA LMS 0.476636 0.772727
190 BTX 0.47541 0.831325
191 5X8 0.474747 0.8
192 7MC 0.474576 0.853659
193 J7C 0.473684 0.7375
194 A3N 0.473684 0.753247
195 YSA 0.473214 0.811765
196 LEU LMS 0.472222 0.772727
197 V3L 0.470588 0.958333
198 NDE 0.469697 0.945946
199 P1H 0.469697 0.864198
200 4YB 0.469565 0.813953
201 KAA 0.46789 0.764045
202 GSU 0.46789 0.811765
203 WSA 0.466102 0.821429
204 SA8 0.465347 0.740741
205 NAJ PZO 0.464 0.884615
206 MAO 0.463918 0.75
207 NDC 0.462687 0.909091
208 SAI 0.460784 0.769231
209 SFG 0.46 0.786667
210 IMO 0.458333 0.890411
211 ZAS 0.457447 0.75641
212 S4M 0.453608 0.659091
213 GJV 0.453608 0.719512
214 7C5 0.452174 0.855263
215 0WD 0.451613 0.909091
216 G A A A 0.451613 0.884615
217 2AM 0.451613 0.878378
218 ARU 0.449541 0.804878
219 A3G 0.447917 0.789474
220 NEC 0.447917 0.736842
221 DSH 0.447917 0.716049
222 SAH 0.446602 0.779221
223 A6D 0.445455 0.73494
224 NA7 0.445455 0.894737
225 NJP 0.443548 0.933333
226 V1N 0.443478 0.958333
227 SMM 0.443396 0.717647
228 F2N 0.442953 0.804598
229 3AT 0.442308 0.905405
230 SAM 0.442308 0.722892
231 FB0 0.441176 0.775281
232 C2R 0.44086 0.891892
233 4TA 0.44 0.841463
234 NAD BBN 0.439716 0.853659
235 EEM 0.438095 0.722892
236 OVE 0.4375 0.844156
237 DCA 0.4375 0.793103
238 U A G G 0.436508 0.896104
239 N6P 0.436364 0.902778
240 MHZ 0.435644 0.689655
241 NAP 0.435115 0.958904
242 AV2 0.433962 0.855263
243 2SA 0.433962 0.92
244 NAD CJ3 0.433566 0.823529
245 TAP 0.431818 0.896104
246 DAT 0.431373 0.844156
247 GEK 0.431193 0.772152
248 AVV 0.431193 0.860759
249 5AD 0.430233 0.736111
250 S7M 0.429907 0.722892
251 NHD 0.428571 0.945205
252 BYC 0.428571 0.795455
253 NA0 0.428571 0.945946
254 DTP 0.428571 0.844156
255 NPW 0.427419 0.875
256 0UM 0.427273 0.731707
257 A3S 0.425743 0.8
258 A7D 0.425743 0.766234
259 AMZ 0.425532 0.878378
260 AAT 0.424528 0.698795
261 FNK 0.423611 0.795455
262 GGZ 0.422018 0.792683
263 PGS 0.421569 0.825
264 KB1 0.421053 0.753086
265 ODP 0.420635 0.897436
266 71V 0.42 0.848101
267 A A A 0.419643 0.893333
268 6C6 0.419048 0.846154
269 N01 0.418605 0.945205
270 6K6 0.418182 0.891892
271 A3T 0.417476 0.810811
272 NDP 0.416 0.909091
273 FAQ 0.415493 0.795455
274 ETB 0.415385 0.802326
275 6IA 0.415094 0.804878
276 FDA 0.414286 0.823529
277 0FQ 0.413793 0.795455
278 TXP 0.412698 0.909091
279 NZQ 0.412698 0.897436
280 FA9 0.411765 0.853659
281 7DD 0.411765 0.917808
282 6FA 0.411348 0.853659
283 APU 0.41129 0.907895
284 Y3J 0.411111 0.716216
285 NFD 0.410853 0.921053
286 62X 0.410714 0.697674
287 P5F 0.410596 0.835294
288 Z5A 0.410448 0.811765
289 1DG 0.410448 0.909091
290 DG1 0.410448 0.909091
291 7D7 0.409091 0.733333
292 COA 0.409091 0.793103
293 0T1 0.409091 0.793103
294 PO4 PO4 A A A A PO4 0.40708 0.916667
295 K15 0.40708 0.714286
296 FAS 0.405594 0.864198
297 FAD 0.405594 0.864198
298 SFD 0.405594 0.744681
299 62F 0.40411 0.851852
300 D5M 0.40404 0.842105
301 DA 0.40404 0.842105
302 AIR 0.402174 0.863014
303 NIA 0.402062 0.790123
304 RGT 0.401709 0.92
305 A U 0.4 0.907895
306 AMX 0.4 0.802326
307 PLP AAD 0.4 0.752809
308 COS 0.4 0.775281
309 FAI 0.4 0.878378
310 ANZ 0.4 0.790123
311 AAM 0.4 0.930556
312 CAO 0.4 0.766667
313 SXZ 0.4 0.743902
314 2MC 0.4 0.741935
315 30N 0.4 0.726316
316 7DT 0.4 0.917808
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RLQ; Ligand: 3SK; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 4rlq.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X1L MET 0.0286 0.42006 1.34875
2 2Y4O DLL 0.000002274 0.44535 4.06321
3 5MST FUM 0.000005955 0.43364 4.23892
4 5MST AMP 0.000002019 0.42446 4.23892
5 2Y4N DLL 0.00006656 0.41842 25.4005
6 4OXI GAP 0.0000001678 0.46211 28.5164
7 5MSD BEZ 0.000001409 0.43193 29.6724
8 5MSD AMP 0.000002847 0.40799 29.6724
9 5C5H 4YB 0.0000006421 0.46616 32.4503
10 5HM3 649 0.0003107 0.40072 36.9942
11 5N9X 8QN 0.0000003809 0.45537 37.7649
12 5N9X ATP 0.00000127 0.43688 37.7649
13 4GR5 APC 0.000002897 0.41756 39.1137
14 1AMU AMP 0.0000001609 0.43588 39.3064
15 3DHV DAL AMP 0.0000006411 0.45032 39.8438
16 4R0M FA5 0.000007137 0.44063 39.8844
17 4FUT ATP 0.00001151 0.40134 40.7555
18 3IES M24 0.000001069 0.48735 40.8478
19 3O84 HTJ 0.000005074 0.43575 40.8478
20 1MDB AMP DBH 0.0000006514 0.43709 41.0405
21 3KXW 1ZZ 0.0000297 0.42077 41.0405
22 4GXQ ATP 0.000004304 0.41703 41.3043
23 2D1S SLU 0.00000005118 0.51219 41.6185
24 5IE3 OXD 0.000001565 0.4644 41.6342
25 5IE3 AMP 0.000001565 0.4644 41.6342
26 4D57 ARG AMP 0.0000003957 0.50754 42.0039
27 1V25 ANP 0.0000003083 0.50563 42.9672
28 5BSR COA 0.00000044 0.54077 44.1233
29 5BSR AMP 0.000003514 0.49279 44.1233
30 3CW9 AMP 0.000000277 0.44031 44.246
31 3CW9 01A 0.0001159 0.40668 44.246
32 1PG4 PRX 0.00000008246 0.55285 45.4721
33 1PG4 COA 0.00000008246 0.55285 45.4721
34 5X8G S0N 0.0000001537 0.54926 47.0103
35 3C5E ATP 0.0000004393 0.53719 47.7842
36 5OE4 3UK 0.00000000002035 0.55227 49.14
Pocket No.: 2; Query (leader) PDB : 4RLQ; Ligand: 3SK; Similar sites found: 74
This union binding pocket(no: 2) in the query (biounit: 4rlq.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TU3 GNP 0.03704 0.40206 None
2 4Q4K FMN 0.005115 0.44601 1.40056
3 2ZKJ ADP 0.03328 0.41653 1.52284
4 1U2Z SAH 0.03091 0.40213 1.84758
5 2GVC FAD 0.04913 0.40232 2.01342
6 3G5S FAD 0.04769 0.40695 2.0316
7 5UQW GDP 0.0272 0.40505 2.1164
8 2I0K FAD 0.04867 0.40455 2.11946
9 1XG5 NAP 0.02401 0.41702 2.15054
10 1TKE SER 0.01817 0.40764 2.23214
11 5MZY 8EZ 0.03622 0.40384 2.41935
12 4B0T ADP 0.02788 0.40592 2.43408
13 4HKP 16B 0.02469 0.40082 2.5641
14 4HKP TKW 0.03073 0.40078 2.5641
15 4RQU NAD 0.01991 0.41898 2.66667
16 3AFN NAP 0.03308 0.4117 2.71318
17 4NBU NAI 0.04074 0.40461 2.8
18 1EK0 GNP 0.03489 0.40078 2.94118
19 3R75 PYR 0.000831 0.42192 3.08285
20 2JAH NDP 0.0334 0.40928 3.23887
21 4NCN GTP 0.01697 0.41422 3.28228
22 5LRT ADP 0.02929 0.40479 3.34646
23 1XSE NDP 0.02751 0.42292 3.38983
24 5TUK FAD 0.03801 0.40272 3.43137
25 4TMZ GSP 0.01974 0.41081 3.46821
26 4K81 GTP 0.02925 0.40753 3.50877
27 2Q2V NAD 0.04257 0.40573 3.52941
28 3VEH 0GA 0.03283 0.41777 3.54767
29 1NVU GTP 0.03008 0.40555 3.61446
30 2C42 PYR 0.01171 0.43252 3.66089
31 2C42 TPP 0.01171 0.43252 3.66089
32 2F1K NAP 0.02842 0.40819 3.94265
33 3OZ2 FAD 0.04311 0.41207 4.03023
34 2JAP NDP 0.03743 0.40661 4.04858
35 1N5D NDP 0.03269 0.40979 4.16667
36 3OID NDP 0.02244 0.42085 4.26357
37 1T9D FAD 0.02653 0.42379 4.4316
38 4RJK TPP 0.01739 0.42083 4.4316
39 2E5V FAD 0.0497 0.41267 4.44915
40 1QZR ANP 0.02457 0.4102 4.54545
41 3C56 PH4 0.0235 0.40365 4.56026
42 1OX5 1PR 0.0266 0.411 4.81696
43 4XOI GTP 0.03323 0.40048 5
44 2IHT TPP 0.03743 0.40051 5.00963
45 1UPA TPP 0.03816 0.40007 5.00963
46 4RVU NDP 0.04281 0.40662 5.12048
47 3A0T ADP 0.01374 0.41386 5.26316
48 1W0J ADP BEF 0.01809 0.4095 5.29412
49 5AE2 FYC 0.04317 0.43 5.58767
50 5AE2 FAD 0.04317 0.43 5.58767
51 1CXZ GSP 0.01266 0.41919 5.81395
52 2FFQ GSP 0.03635 0.40119 5.84795
53 5IRR GSP 0.02151 0.40728 6.16883
54 5O2T GSP 0.03706 0.40074 6.41711
55 2W2X GSP 0.01781 0.40984 6.45161
56 2HF9 GSP 0.02287 0.41045 6.63717
57 3H0L ADP 0.006811 0.41589 7.44681
58 4KVG GTP 0.0346 0.40097 8.07692
59 2Z6J FMN 0.0345 0.40619 8.43373
60 5T79 NDP 0.02252 0.41486 9.33735
61 5B48 TDN 0.02017 0.41991 10.1639
62 5UFQ GNP 0.0288 0.4007 11.4754
63 1E6E FAD 0.04829 0.40571 11.7188
64 2UZI GTP 0.03005 0.40421 12.2807
65 4D0G GTP 0.01859 0.41057 13.1429
66 2CK3 ADP 0.02139 0.409 14
67 2CK3 ANP 0.02319 0.40221 14
68 1DQX BMP 0.01695 0.41264 14.9813
69 2C5L GTP 0.02365 0.41108 16.2393
70 3OII SAH 0.02271 0.40441 17.3913
71 4HIA FMN 0.02352 0.42082 21.0227
72 4DG8 AMP 0.006748 0.42559 29.8651
73 5EY9 5SV 0.004148 0.45077 37.9576
74 3E7W AMP 0.005637 0.42732 42.8571
Feedback