Receptor
PDB id Resolution Class Description Source Keywords
3CW8 2.25 Å EC: 6.2.1.33 4-CHLOROBENZOYL-COA LIGASE/SYNTHETASE, BOUND TO 4CBA-ADENYLA ALCALIGENES SP. ADENYLATE-FORMING ENZYMES ACYL-COA LIGASE LIGASE
Ref.: STRUCTURAL CHARACTERIZATION OF A 140 DEGREES DOMAIN IN THE TWO-STEP REACTION CATALYZED BY 4-CHLOROBENZO LIGASE. BIOCHEMISTRY V. 47 8016 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
00A X:909;
 Valid;
 none;
 submit data
485.772 C17 H17 Cl N5 O8 P c1cc(...
EDO X:801;
X:802;
X:803;
X:804;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CW9 2 Å EC: 6.2.1.33 4-CHLOROBENZOYL-COA LIGASE/SYNTHETASE IN THE THIOESTER-FORMI CONFORMATION, BOUND TO 4-CHLOROPHENACYL-COA ALCALIGENES SP. ADENYLATE-FORMING ENZYMES ACYL-COA LIGASE DOMAIN ALTERNATILIGASE
Ref.: STRUCTURAL CHARACTERIZATION OF A 140 DEGREES DOMAIN IN THE TWO-STEP REACTION CATALYZED BY 4-CHLOROBENZO LIGASE. BIOCHEMISTRY V. 47 8016 2008
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3CW9 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 1T5D - 174 C7 H5 Cl O2 c1cc(ccc1C....
3 2QVZ - 3BZ C7 H5 Cl O2 c1cc(cc(c1....
4 3CW8 - 00A C17 H17 Cl N5 O8 P c1cc(ccc1C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3CW9 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 1T5D - 174 C7 H5 Cl O2 c1cc(ccc1C....
3 2QVZ - 3BZ C7 H5 Cl O2 c1cc(cc(c1....
4 3CW8 - 00A C17 H17 Cl N5 O8 P c1cc(ccc1C....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3CW9 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 1T5D - 174 C7 H5 Cl O2 c1cc(ccc1C....
3 2QVZ - 3BZ C7 H5 Cl O2 c1cc(cc(c1....
4 3CW8 - 00A C17 H17 Cl N5 O8 P c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 00A; Similar ligands found: 307
No: Ligand ECFP6 Tc MDL keys Tc
1 00A 1 1
2 OOB 0.816092 0.946667
3 CA0 0.729412 0.909091
4 A2D 0.710843 0.907895
5 3UK 0.694737 0.934211
6 BA3 0.694118 0.907895
7 AP5 0.686047 0.907895
8 ADP 0.686047 0.883117
9 B4P 0.686047 0.907895
10 5AL 0.681319 0.921053
11 AN2 0.678161 0.871795
12 M33 0.670455 0.871795
13 AD9 0.666667 0.860759
14 9SN 0.666667 0.961039
15 SRP 0.666667 0.897436
16 ATP 0.662921 0.883117
17 ACP 0.662921 0.860759
18 AQP 0.655556 0.883117
19 APR 0.655556 0.907895
20 AR6 0.655556 0.907895
21 5FA 0.655556 0.883117
22 AMP 0.654762 0.881579
23 A 0.654762 0.881579
24 WAQ 0.653061 0.875
25 ADX 0.651685 0.8
26 DLL 0.649485 0.946667
27 SAP 0.648352 0.839506
28 AGS 0.648352 0.839506
29 1ZZ 0.646465 0.833333
30 8QN 0.645833 0.921053
31 50T 0.644444 0.848101
32 PAJ 0.639175 0.853659
33 AMO 0.639175 0.897436
34 4AD 0.639175 0.886076
35 PRX 0.637363 0.8375
36 ANP 0.634409 0.860759
37 ACQ 0.634409 0.860759
38 ABM 0.632184 0.858974
39 TXA 0.63 0.897436
40 SRA 0.627907 0.8375
41 ATF 0.621053 0.897436
42 AMP MG 0.62069 0.835443
43 LAD 0.62 0.853659
44 PR8 0.62 0.843373
45 A22 0.618557 0.896104
46 A12 0.617977 0.85
47 AP2 0.617977 0.85
48 AHX 0.616162 0.841463
49 PTJ 0.613861 0.864198
50 ME8 0.613861 0.833333
51 NB8 0.613861 0.864198
52 FA5 0.61165 0.922078
53 YAP 0.61165 0.910256
54 OAD 0.61 0.909091
55 ADQ 0.606061 0.909091
56 GAP 0.6 0.884615
57 3OD 0.598039 0.909091
58 AU1 0.597826 0.860759
59 LAQ 0.592593 0.833333
60 A1R 0.59 0.829268
61 SON 0.586957 0.897436
62 DAL AMP 0.585859 0.896104
63 APC 0.585106 0.85
64 4UV 0.584906 0.910256
65 M24 0.584746 0.936709
66 TAT 0.583333 0.85
67 ADP MG 0.580645 0.848101
68 25A 0.58 0.907895
69 5SV 0.58 0.797619
70 ADV 0.578947 0.873418
71 RBY 0.578947 0.873418
72 ADP BEF 0.574468 0.85
73 BEF ADP 0.574468 0.85
74 4UU 0.574074 0.910256
75 4UW 0.567568 0.876543
76 NXX 0.567568 0.922078
77 DND 0.567568 0.922078
78 BIS 0.567308 0.875
79 FYA 0.567308 0.871795
80 TYM 0.5625 0.922078
81 ADP PO3 0.5625 0.881579
82 25L 0.561905 0.896104
83 IOT 0.561404 0.804598
84 XAH 0.560748 0.811765
85 YLP 0.558559 0.813953
86 ATP MG 0.556701 0.848101
87 6V0 0.553571 0.864198
88 NAX 0.553571 0.843373
89 G3A 0.550459 0.864198
90 OMR 0.548673 0.823529
91 MYR AMP 0.54717 0.811765
92 G5P 0.545455 0.864198
93 48N 0.544643 0.864198
94 YLC 0.54386 0.833333
95 YLB 0.54386 0.813953
96 YLA 0.543103 0.813953
97 ALF ADP 0.54 0.8625
98 ADP ALF 0.54 0.8625
99 NAI 0.539823 0.875
100 TXD 0.539823 0.875
101 MAP 0.539216 0.839506
102 CNA 0.538462 0.897436
103 DZD 0.537815 0.853659
104 BT5 0.537815 0.804598
105 TXE 0.535088 0.875
106 ANP MG 0.534653 0.839506
107 VO4 ADP 0.534653 0.871795
108 ADP VO4 0.534653 0.871795
109 AOC 0.532609 0.769231
110 TYR AMP 0.53211 0.897436
111 AFH 0.531532 0.924051
112 PAP 0.530612 0.87013
113 5CD 0.529412 0.8
114 NAD 0.529412 0.921053
115 GTA 0.526786 0.833333
116 AYB 0.525424 0.804598
117 A3D 0.520661 0.909091
118 ADP BMA 0.518868 0.884615
119 T5A 0.516949 0.813953
120 A3P 0.515789 0.881579
121 ATR 0.515152 0.857143
122 A A 0.514019 0.883117
123 UP5 0.513043 0.886076
124 ADN 0.511905 0.766234
125 XYA 0.511905 0.766234
126 RAB 0.511905 0.766234
127 5AS 0.510417 0.736264
128 G5A 0.51 0.755556
129 ZID 0.507937 0.909091
130 DTA 0.505618 0.759494
131 2A5 0.50505 0.814815
132 SSA 0.504854 0.755556
133 LPA AMP 0.504348 0.811765
134 4TC 0.504274 0.864198
135 AP0 0.504274 0.841463
136 COD 0.504132 0.766667
137 3AM 0.5 0.844156
138 A4P 0.5 0.795455
139 A2R 0.5 0.896104
140 PPS 0.5 0.77907
141 TAD 0.5 0.831325
142 5N5 0.5 0.74359
143 YLY 0.496 0.804598
144 ARG AMP 0.495652 0.802326
145 ATP A A A 0.495495 0.894737
146 JB6 0.495413 0.851852
147 TSB 0.495238 0.772727
148 A5A 0.495146 0.781609
149 EP4 0.494382 0.707317
150 A4D 0.494253 0.74359
151 NAE 0.492063 0.886076
152 139 0.491667 0.843373
153 ADJ 0.491667 0.823529
154 UPA 0.491525 0.875
155 7MD 0.491228 0.833333
156 7D3 0.489583 0.802469
157 EAD 0.488372 0.843373
158 NAQ 0.488189 0.864198
159 AMP DBH 0.486726 0.860759
160 52H 0.485714 0.755556
161 VMS 0.485714 0.764045
162 54H 0.485714 0.764045
163 6AD 0.485437 0.809524
164 7D4 0.484848 0.802469
165 ITT 0.484848 0.833333
166 A2P 0.484536 0.868421
167 N0B 0.484375 0.835294
168 AHZ 0.482759 0.811765
169 53H 0.481132 0.755556
170 5CA 0.481132 0.755556
171 7D5 0.478261 0.8
172 P1H 0.473684 0.823529
173 6RE 0.473684 0.694118
174 3DH 0.473118 0.725
175 AMP NAD 0.472868 0.897436
176 P5A 0.472727 0.723404
177 M2T 0.472527 0.690476
178 LSS 0.472222 0.73913
179 DSZ 0.472222 0.775281
180 NSS 0.472222 0.755556
181 NAD IBO 0.471545 0.8625
182 ALF ADP 3PG 0.470588 0.876543
183 AF3 ADP 3PG 0.470588 0.876543
184 LA8 ALF 3PG 0.470588 0.876543
185 SA8 0.470588 0.705882
186 NVA LMS 0.46789 0.73913
187 BTX 0.467742 0.793103
188 MTA 0.467391 0.725
189 7MC 0.466667 0.813953
190 AR6 AR6 0.465517 0.907895
191 5X8 0.465347 0.759494
192 SFG 0.465347 0.746835
193 YSA 0.464912 0.775281
194 A3N 0.463918 0.716049
195 J7C 0.463918 0.702381
196 LEU LMS 0.463636 0.73913
197 NA7 0.463636 0.85
198 NDE 0.462687 0.897436
199 NJP 0.459677 0.886076
200 KAA 0.459459 0.731183
201 GSU 0.459459 0.775281
202 2AM 0.457447 0.833333
203 7C5 0.456897 0.8125
204 A5D 0.456311 0.759494
205 0WD 0.456 0.864198
206 FB0 0.455882 0.741935
207 NDC 0.455882 0.864198
208 ARU 0.454545 0.809524
209 MAO 0.454545 0.715909
210 NAJ PYZ 0.453846 0.9125
211 SAH 0.451923 0.740741
212 SAI 0.451923 0.731707
213 IMO 0.44898 0.844156
214 ZAS 0.447917 0.719512
215 3AT 0.447619 0.858974
216 V3L 0.447619 0.907895
217 NAJ PZO 0.445312 0.841463
218 GJV 0.444444 0.686047
219 S4M 0.444444 0.630435
220 G A A A 0.444444 0.841463
221 NPW 0.443548 0.833333
222 EEM 0.443396 0.689655
223 NZQ 0.44 0.853659
224 AV2 0.439252 0.8125
225 A3G 0.438776 0.75
226 DSH 0.438776 0.682353
227 4YB 0.436975 0.777778
228 DAT 0.436893 0.802469
229 ODP 0.436508 0.853659
230 AVV 0.436364 0.8875
231 SMM 0.435185 0.685393
232 S7M 0.435185 0.689655
233 WSA 0.434426 0.784091
234 DTP 0.433962 0.802469
235 SAM 0.433962 0.689655
236 4TA 0.433071 0.802326
237 0UM 0.432432 0.697674
238 NDP 0.432 0.864198
239 DCA 0.430769 0.758242
240 U A G G 0.429688 0.851852
241 OVE 0.428571 0.802469
242 TXP 0.428571 0.864198
243 NAP 0.428571 0.909091
244 FNK 0.427586 0.76087
245 MHZ 0.427184 0.659341
246 2SA 0.425926 0.873418
247 6FA 0.425532 0.813953
248 DG1 0.425373 0.864198
249 TAP 0.425373 0.851852
250 1DG 0.425373 0.864198
251 A6D 0.424779 0.701149
252 01A 0.424658 0.804348
253 NEC 0.424242 0.7
254 649 0.422764 0.741935
255 NA0 0.422222 0.897436
256 5AD 0.420455 0.697368
257 ETB 0.419847 0.766667
258 FAS 0.41958 0.823529
259 SFD 0.41958 0.714286
260 FAD 0.41958 0.823529
261 FDA 0.41844 0.786517
262 Y3J 0.417582 0.723684
263 7DD 0.417476 0.87013
264 A3S 0.417476 0.759494
265 A7D 0.417476 0.728395
266 AAT 0.416667 0.666667
267 C2R 0.416667 0.846154
268 AMZ 0.416667 0.833333
269 62X 0.415929 0.666667
270 FAY 0.414966 0.833333
271 P5F 0.414474 0.797753
272 GGZ 0.414414 0.755814
273 KB1 0.413793 0.780488
274 NAD BBN 0.413793 0.813953
275 0T1 0.413534 0.758242
276 COA 0.413534 0.758242
277 PGS 0.413462 0.785714
278 A A A 0.412281 0.848101
279 K15 0.412281 0.681818
280 RFL 0.412162 0.795455
281 V1N 0.411765 0.907895
282 71V 0.411765 0.807229
283 6C6 0.411215 0.804878
284 XNP 0.410853 0.821429
285 NHD 0.410853 0.896104
286 GEK 0.410714 0.73494
287 A3T 0.409524 0.769231
288 F2N 0.409091 0.769231
289 FAM 0.408759 0.78022
290 NAD CJ3 0.408163 0.786517
291 62F 0.408163 0.811765
292 6IA 0.407407 0.767442
293 AAM 0.405941 0.881579
294 7DT 0.40566 0.87013
295 APU 0.404762 0.8625
296 30N 0.404412 0.69697
297 Z5A 0.404412 0.775281
298 CAO 0.404412 0.734043
299 AMX 0.404412 0.766667
300 COS 0.404412 0.741935
301 N6P 0.403509 0.855263
302 FYN 0.402878 0.758242
303 CMX 0.40146 0.777778
304 SCO 0.40146 0.777778
305 7D7 0.4 0.696203
306 SOP 0.4 0.741935
307 PO4 PO4 A A A A PO4 0.4 0.868421
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CW9; Ligand: 01A; Similar sites found: 23
This union binding pocket(no: 1) in the query (biounit: 3cw9.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5M0T AKG 0.03854 0.40097 2.72109
2 2GUC MAN 0.001445 0.46984 4.91803
3 3KXW 1ZZ 0.001042 0.41818 10.1695
4 5EY9 5SV 0.0006374 0.42232 15.0794
5 2Y4N DLL 0.004247 0.40008 18.7643
6 4OXI GAP 0.0005069 0.40758 28.7698
7 2D1S SLU 0.003171 0.40638 31.746
8 5MST FUM 0.0006057 0.41781 31.9444
9 5MSD BEZ 0.0004461 0.40167 32.3413
10 1PG4 PRX 0.000001882 0.55456 39.2857
11 1PG4 COA 0.000001882 0.55456 39.2857
12 1V25 ANP 0.002326 0.41683 41.6667
13 3IES M24 0.004051 0.40727 41.6667
14 3C5E ATP 0.00001261 0.52874 42.4603
15 3O84 HTJ 0.0002064 0.44079 42.6587
16 4D57 ARG AMP 0.0004919 0.44488 43.8492
17 4RLQ 3SK 0.0001159 0.40668 44.246
18 3NYQ MCA 0.0000000101 0.62492 46.1386
19 3NYQ AMP 0.00000001148 0.62492 46.1386
20 5C5H 4YB 0.00008547 0.4593 46.3576
21 5BSR COA 0.0000001954 0.60827 47.619
22 5BSR AMP 0.003115 0.41947 47.619
23 5X8G S0N 0.000000003064 0.67559 49.2784
Pocket No.: 2; Query (leader) PDB : 3CW9; Ligand: AMP; Similar sites found: 56
This union binding pocket(no: 2) in the query (biounit: 3cw9.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3E1T FAD 0.02613 0.40553 0.992063
2 1RWQ 5AP 0.0125 0.4144 1.5873
3 1R6T TYM 0.02099 0.40369 2.57937
4 5BVE 4VG 0.03694 0.40747 2.77008
5 4EPM AMP 0.0004084 0.42262 3.37302
6 3ABI NAD 0.0108 0.41049 3.56164
7 5KOD AMP 0.00006527 0.47769 3.96825
8 3QOX SAH 0.01023 0.40318 4.92958
9 4BLW SAH 0.01411 0.4012 5.88235
10 2C91 NAP 0.01802 0.40475 6.34921
11 4B2G V1N 0.0002126 0.47674 7.7381
12 5D6J ATP 0.00001408 0.52193 7.93651
13 3GD4 FAD 0.04421 0.40352 8.73016
14 2BP1 NDP 0.01783 0.40497 9.72222
15 3KXW 1ZZ 0.000003361 0.56625 10.1695
16 1GVE NAP 0.02082 0.4007 12.844
17 5HM3 649 0.00001582 0.43128 14.881
18 5EY9 5SV 0.0003334 0.47364 15.0794
19 2Y4O DLL 0.000000004781 0.68725 18.0587
20 2Y4N DLL 0.000002233 0.57848 18.7643
21 2Y4N PAC 0.00001867 0.52155 18.7643
22 4R0M FA5 0.0000002128 0.62079 23.4127
23 4DG8 AMP 0.000005373 0.53037 27.1825
24 4OXI GAP 0.000000004425 0.68244 28.7698
25 3E7W AMP 0.00000003981 0.60962 29.9603
26 2D1S SLU 0.0000000452 0.65854 31.746
27 5MST FUM 0.00000004345 0.647 31.9444
28 5MST AMP 0.00000002078 0.64609 31.9444
29 5MSD AMP 0.000000005937 0.65508 32.3413
30 5MSD BEZ 0.00000001548 0.65508 32.3413
31 4FUT ATP 0.0000001009 0.61915 38.8889
32 4GXQ ATP 0.00000003702 0.58914 38.8889
33 1PG4 PRX 0.000000008502 0.71963 39.2857
34 1PG4 COA 0.000000008502 0.71963 39.2857
35 5OE4 3UK 0.0000003007 0.60113 40.2948
36 1V25 ANP 0.00000001047 0.69677 41.6667
37 3IES M24 0.00000001557 0.68869 41.6667
38 3DHV DAL AMP 0.00000001225 0.66281 41.6667
39 4GR5 APC 0.0000007046 0.59148 42.0635
40 3C5E ATP 0.0000004345 0.6465 42.4603
41 3O84 HTJ 0.00003694 0.51693 42.6587
42 1AMU AMP 0.000000004584 0.65922 42.8571
43 4D57 ARG AMP 0.000000005216 0.71305 43.8492
44 1RY2 AMP 0.000000004527 0.64632 44.246
45 1MDB AMP DBH 0.0000007788 0.57999 44.246
46 4RLQ 3SK 0.000000277 0.44031 44.246
47 5N9X 8QN 0.0000000001084 0.75756 44.8413
48 5N9X ATP 0.000000002092 0.69688 44.8413
49 5IE3 OXD 0.00000004153 0.65793 45.2381
50 5IE3 AMP 0.00000004153 0.65793 45.2381
51 3NYQ AMP 0.0000001449 0.64141 46.1386
52 3NYQ MCA 0.0000001407 0.64 46.1386
53 5C5H 4YB 0.000003825 0.56369 46.3576
54 5BSR AMP 0.000001567 0.60611 47.619
55 5BSR COA 0.000003379 0.60611 47.619
56 5X8G S0N 0.00000000346 0.74497 49.2784
Pocket No.: 3; Query (leader) PDB : 3CW9; Ligand: AMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3cw9.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3CW9; Ligand: 01A; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3cw9.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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