Receptor
PDB id Resolution Class Description Source Keywords
5BSU 1.75 Å EC: 6.2.1.12 CRYSTAL STRUCTURE OF 4-COUMARATE:COA LIGASE COMPLEXED WITH C ADENYLATE NICOTIANA TABACUM 4-COUMARATE:COA LIGASE LIGASE
Ref.: STRUCTURAL BASIS FOR SPECIFICITY AND FLEXIBILITY IN 4-COUMARATE:COA LIGASE. STRUCTURE V. 23 2032 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4UV A:601;
Valid;
none;
submit data
507.347 C19 H18 N5 O10 P c1nc(...
MG A:603;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
GOL A:602;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5BSR 1.5 Å EC: 6.2.1.12 CRYSTAL STRUCTURE OF 4-COUMARATE:COA LIGASE COMPLEXED WITH A MONOPHOSPHATE AND COENZYME A NICOTIANA TABACUM 4-COUMARATE:COA LIGASE LIGASE
Ref.: STRUCTURAL BASIS FOR SPECIFICITY AND FLEXIBILITY IN 4-COUMARATE:COA LIGASE. STRUCTURE V. 23 2032 2015
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5BSV - 4UW C20 H22 N5 O10 P COC1=CC(=C....
2 5BSW - 4UW C20 H22 N5 O10 P COC1=CC(=C....
3 5BST - 4UU C19 H20 N5 O9 P c1nc(c2c(n....
4 5BSU - 4UV C19 H18 N5 O10 P c1nc(c2c(n....
5 5BSM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 5BSR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5BSV - 4UW C20 H22 N5 O10 P COC1=CC(=C....
2 5BSW - 4UW C20 H22 N5 O10 P COC1=CC(=C....
3 5BST - 4UU C19 H20 N5 O9 P c1nc(c2c(n....
4 5BSU - 4UV C19 H18 N5 O10 P c1nc(c2c(n....
5 5BSM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 5BSR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5BSV - 4UW C20 H22 N5 O10 P COC1=CC(=C....
2 5BSW - 4UW C20 H22 N5 O10 P COC1=CC(=C....
3 5BST - 4UU C19 H20 N5 O9 P c1nc(c2c(n....
4 5BSU - 4UV C19 H18 N5 O10 P c1nc(c2c(n....
5 5BSM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 5BSR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4UV; Similar ligands found: 247
No: Ligand ECFP6 Tc MDL keys Tc
1 4UV 1 1
2 4UU 0.762376 1
3 4UW 0.700935 0.961039
4 CA0 0.666667 0.921053
5 5AL 0.642857 0.933333
6 A2D 0.630435 0.92
7 BA3 0.617021 0.92
8 SRP 0.613861 0.909091
9 8QN 0.61165 0.933333
10 OOB 0.61165 0.959459
11 B4P 0.610526 0.92
12 ADP 0.610526 0.894737
13 AP5 0.610526 0.92
14 AN2 0.604167 0.883117
15 PRX 0.602041 0.848101
16 ANP 0.6 0.871795
17 DLL 0.6 0.959459
18 1ZZ 0.598131 0.843373
19 ADX 0.597938 0.809524
20 M33 0.597938 0.883117
21 A 0.597826 0.893333
22 AMP 0.597826 0.893333
23 AD9 0.59596 0.871795
24 3UK 0.59434 0.946667
25 ACP 0.591837 0.871795
26 50T 0.591837 0.858974
27 ATP 0.591837 0.894737
28 4AD 0.590476 0.897436
29 AMO 0.590476 0.909091
30 PAJ 0.590476 0.864198
31 WAQ 0.588785 0.886076
32 AQP 0.585859 0.894737
33 AR6 0.585859 0.92
34 APR 0.585859 0.92
35 5FA 0.585859 0.894737
36 00A 0.584906 0.910256
37 ME8 0.583333 0.843373
38 AGS 0.58 0.85
39 SAP 0.58 0.85
40 ABM 0.578947 0.87013
41 LAD 0.574074 0.864198
42 PR8 0.574074 0.853659
43 ATF 0.572816 0.860759
44 PTJ 0.568807 0.875
45 TXA 0.568807 0.909091
46 NB8 0.568807 0.875
47 GAP 0.568627 0.896104
48 ACQ 0.568627 0.871795
49 AMP MG 0.568421 0.846154
50 FA5 0.567568 0.934211
51 AP2 0.56701 0.860759
52 A12 0.56701 0.860759
53 5SV 0.566038 0.807229
54 AU1 0.565657 0.871795
55 9SN 0.558559 0.898734
56 SRA 0.557895 0.848101
57 AHX 0.555556 0.851852
58 SON 0.555556 0.909091
59 YAP 0.553571 0.922078
60 TAT 0.553398 0.860759
61 OAD 0.550459 0.921053
62 ADQ 0.546296 0.921053
63 YLC 0.546219 0.865854
64 A22 0.542056 0.907895
65 3OD 0.540541 0.921053
66 BIS 0.540541 0.839506
67 APC 0.539216 0.860759
68 IOT 0.53719 0.813953
69 25A 0.537037 0.92
70 ADP MG 0.534653 0.858974
71 ADV 0.533981 0.884615
72 RBY 0.533981 0.884615
73 A1R 0.53211 0.839506
74 ADP BEF 0.529412 0.8375
75 BEF ADP 0.529412 0.8375
76 MAP 0.527778 0.85
77 DAL AMP 0.527778 0.907895
78 FYA 0.526786 0.883117
79 G3A 0.525862 0.875
80 LAQ 0.525424 0.843373
81 TYM 0.525 0.934211
82 MYR AMP 0.522124 0.821429
83 XAH 0.521739 0.821429
84 G5P 0.521368 0.875
85 YLP 0.521008 0.823529
86 ADP PO3 0.519231 0.893333
87 GTA 0.516949 0.843373
88 UP5 0.516667 0.922078
89 ATP MG 0.514286 0.858974
90 OMR 0.512397 0.833333
91 ADP VO4 0.509259 0.883117
92 VO4 ADP 0.509259 0.883117
93 25L 0.508772 0.907895
94 48N 0.508333 0.875
95 4TC 0.508197 0.898734
96 UPA 0.508197 0.910256
97 YLB 0.508197 0.823529
98 139 0.508065 0.876543
99 6V0 0.504132 0.948052
100 NAX 0.504132 0.924051
101 ALF ADP 0.5 0.82716
102 ADP ALF 0.5 0.82716
103 YLA 0.496 0.845238
104 AFH 0.495798 0.864198
105 ANP MG 0.495413 0.85
106 BT5 0.492188 0.813953
107 AYB 0.492063 0.813953
108 CNA 0.492063 0.909091
109 A4P 0.491935 0.847059
110 DND 0.491803 0.934211
111 NXX 0.491803 0.934211
112 TXD 0.491803 0.910256
113 NAI 0.491803 0.960526
114 TXE 0.487805 0.910256
115 COD 0.484375 0.775281
116 T5A 0.484127 0.890244
117 RAB 0.483516 0.776316
118 ADN 0.483516 0.776316
119 XYA 0.483516 0.776316
120 TYR AMP 0.483051 0.909091
121 ADP BMA 0.482456 0.896104
122 TAD 0.479339 0.841463
123 A A 0.478261 0.894737
124 M24 0.477273 0.876543
125 AOC 0.475248 0.802632
126 ATP A A A 0.474576 0.906667
127 NAD 0.472868 0.933333
128 A5A 0.472727 0.790698
129 G5A 0.472222 0.764045
130 5AS 0.471154 0.744444
131 5CD 0.468085 0.763158
132 A4D 0.468085 0.753247
133 2A5 0.46729 0.825
134 N0B 0.466667 0.86747
135 YLY 0.466165 0.813953
136 A3D 0.465649 0.921053
137 ARG AMP 0.463415 0.811765
138 PAP 0.462963 0.881579
139 ITT 0.462264 0.844156
140 BTX 0.461538 0.802326
141 JB6 0.461538 0.8625
142 A3P 0.461538 0.893333
143 ADJ 0.460938 0.901235
144 AP0 0.460317 0.923077
145 5CA 0.460177 0.764045
146 TSB 0.460177 0.781609
147 LPA AMP 0.459677 0.821429
148 7MD 0.459016 0.843373
149 5N5 0.457447 0.753247
150 SSA 0.455357 0.764045
151 AMP DBH 0.454545 0.871795
152 NAE 0.451852 0.897436
153 AHZ 0.451613 0.821429
154 VMS 0.451327 0.772727
155 54H 0.451327 0.772727
156 52H 0.451327 0.764045
157 PPS 0.45045 0.788235
158 G A A A 0.450382 0.851852
159 ATR 0.449541 0.868421
160 DTA 0.44898 0.769231
161 NAQ 0.448529 0.875
162 53H 0.447368 0.764045
163 AR6 AR6 0.447154 0.92
164 3AM 0.445545 0.855263
165 5X8 0.444444 0.769231
166 MTA 0.444444 0.734177
167 J7C 0.442308 0.710843
168 A3N 0.442308 0.746835
169 AF3 ADP 3PG 0.440945 0.841463
170 LA8 ALF 3PG 0.440945 0.841463
171 ALF ADP 3PG 0.440945 0.841463
172 P5A 0.440678 0.731183
173 7D5 0.44 0.810127
174 LSS 0.439655 0.747253
175 DSZ 0.439655 0.784091
176 NSS 0.439655 0.764045
177 EAD 0.438849 0.924051
178 EP4 0.438776 0.716049
179 A2R 0.438596 0.907895
180 7D3 0.438095 0.8125
181 7MC 0.4375 0.823529
182 6AD 0.4375 0.819277
183 6RE 0.436893 0.702381
184 U A G G 0.43609 0.8625
185 DZD 0.43609 0.864198
186 NVA LMS 0.435897 0.747253
187 3DH 0.435644 0.734177
188 7D4 0.435185 0.8125
189 ZID 0.434783 0.921053
190 M2T 0.434343 0.698795
191 A2P 0.433962 0.88
192 LEU LMS 0.432203 0.747253
193 NAD IBO 0.431818 0.873418
194 NDC 0.430556 0.875
195 IMO 0.428571 0.855263
196 V3L 0.428571 0.92
197 KAA 0.428571 0.73913
198 GSU 0.428571 0.784091
199 7C5 0.427419 0.822785
200 ZAS 0.427184 0.728395
201 P1H 0.426573 0.901235
202 SFD 0.425676 0.721649
203 AAT 0.424779 0.714286
204 AMP NAD 0.42446 0.909091
205 ARU 0.423729 0.776471
206 YSA 0.422764 0.784091
207 AV2 0.421053 0.822785
208 FB0 0.42069 0.75
209 MAO 0.420561 0.724138
210 NAJ PZO 0.419118 0.923077
211 649 0.418605 0.75
212 SFG 0.418182 0.75641
213 4TA 0.41791 0.878049
214 SMM 0.417391 0.693182
215 NAJ PYZ 0.417266 0.853659
216 NDE 0.416667 0.909091
217 A U 0.412214 0.897436
218 6FA 0.412162 0.823529
219 GJV 0.411215 0.694118
220 S4M 0.411215 0.637363
221 A5D 0.410714 0.769231
222 SA8 0.410714 0.714286
223 NAD BBN 0.410596 0.823529
224 ODP 0.410448 0.8875
225 4YB 0.409449 0.786517
226 U G A 0.409396 0.843373
227 NA7 0.408333 0.860759
228 2AM 0.407767 0.844156
229 WSA 0.407692 0.793103
230 0WD 0.407407 0.948052
231 SAH 0.40708 0.75
232 SAI 0.40708 0.740741
233 DSH 0.40566 0.690476
234 A3G 0.40566 0.759494
235 NEC 0.40566 0.708861
236 FDA 0.405405 0.837209
237 FNK 0.405229 0.808989
238 NAD CJ3 0.405229 0.795455
239 3AT 0.403509 0.87013
240 SAM 0.403509 0.697674
241 PUA 0.402878 0.864198
242 P5F 0.402516 0.827586
243 APU 0.401515 0.897436
244 EEM 0.4 0.697674
245 N6P 0.4 0.866667
246 5AD 0.4 0.706667
247 NJP 0.4 0.897436
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5BSR; Ligand: COA; Similar sites found: 70
This union binding pocket(no: 1) in the query (biounit: 5bsr.bio1) has 55 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YQT ADP 0.03934 0.42491 2.04461
2 3HQP FDP 0.03654 0.41563 2.40481
3 2HHP FLC 0.002279 0.4322 2.64151
4 2ZWI C5P 0.03635 0.41919 2.68097
5 1JPA ANP 0.03726 0.42425 2.88462
6 1G27 BB1 0.0165 0.42061 2.97619
7 4NST ADP 0.04339 0.40267 2.98507
8 3JQ3 ADP 0.03206 0.42218 3.00546
9 4DS0 A2G GAL NAG FUC 0.001844 0.51241 3.06748
10 2X1L ADN 0.04863 0.41225 3.43511
11 4YH2 GSH 0.03146 0.42636 3.6036
12 5EFQ ADP 0.04187 0.40345 3.7464
13 4RI6 GSH 0.01897 0.43858 4.65116
14 3W6X HZP 0.04397 0.42369 4.80349
15 5EGM 5NY 0.03477 0.40208 4.83871
16 2J5V RGP 0.0155 0.452 4.90463
17 5F6U 5VK 0.03984 0.42154 5.09554
18 4EPM AMP 0.005469 0.43129 5.35055
19 1M2X MCO 0.03098 0.43613 5.38117
20 1KTG AMP 0.04715 0.41963 6.52174
21 5JY4 ISC 0.03103 0.41297 6.90537
22 4B2G V1N 0.002118 0.45319 7.01107
23 3W9R A8S 0.04947 0.40857 7.40741
24 5KOD AMP 0.000622 0.5038 7.56458
25 4JX1 CAH 0.04135 0.41118 8.84956
26 1V7Z CRN 0.0484 0.41236 10
27 1S17 GNR 0.0202 0.41632 11.1111
28 2NUO BGC 0.04182 0.42936 11.4754
29 2Y4N DLL 0.000003816 0.54924 12.5858
30 2Y4N PAC 0.00003569 0.53945 12.5858
31 3IWD M2T 0.03546 0.42365 14.5161
32 3N5O GSH 0.009313 0.43272 15.3191
33 4DG8 AMP 0.000001097 0.63764 24.5387
34 5N9X ATP 0.00000128 0.60694 25.3308
35 5N9X 8QN 0.00000116 0.60282 25.3308
36 5N9X THR 0.0005505 0.53594 25.3308
37 4DR9 BB2 0.03985 0.4074 28.125
38 5MST AMP 0.0000006471 0.63431 30.2583
39 5MST FUM 0.000001252 0.58985 30.2583
40 2Y4O DLL 0.0000003592 0.61991 33.1828
41 5HM3 649 0.00001645 0.51889 34.1328
42 5EY9 5SV 0.0000334 0.52227 34.3173
43 5OE4 3UK 0.0000001173 0.65542 35.1351
44 5MSD AMP 0.00000007911 0.69519 35.7934
45 5MSD BEZ 0.00000006074 0.67626 35.7934
46 4R0M FA5 0.0000001305 0.42925 35.7934
47 3NYQ MCA 0.0000000002766 0.7009 37.0297
48 3NYQ AMP 0.0000000002348 0.6973 37.0297
49 4GR5 APC 0.000002684 0.62546 37.4539
50 3E7W AMP 0.0000316 0.57037 38.9432
51 3DHV DAL AMP 0.000001576 0.60274 40.4297
52 4OXI GAP 0.0000001233 0.40846 41.3284
53 4GXQ ATP 0.0000003935 0.63087 41.502
54 1AMU AMP 0.000002309 0.62135 41.5129
55 4D57 ARG AMP 0.000000007386 0.62804 41.6974
56 3O84 HTJ 0.0000001267 0.62782 41.6974
57 5C5H 4YB 0.0000004178 0.59968 41.7219
58 4FUT ATP 0.000000899 0.6206 41.9483
59 1MDB AMP DBH 0.000000237 0.64813 42.6716
60 3C5E ATP 0.0000003752 0.50679 43.1734
61 3KXW 1ZZ 0.000002037 0.57017 43.5424
62 1PG4 COA 0.000000289 0.53278 43.7269
63 1PG4 PRX 0.000000289 0.53278 43.7269
64 1V25 ANP 0.00000000365 0.64509 43.9926
65 4RLQ 3SK 0.00000044 0.54077 44.1233
66 3CW9 01A 0.0000001954 0.60827 47.619
67 3CW9 AMP 0.000003379 0.60611 47.619
68 2D1S SLU 0.0000001754 0.5996 49.4465
69 5IE3 OXD 0.0000001137 0.4378 49.6109
70 5IE3 AMP 0.0000001137 0.4378 49.6109
Pocket No.: 2; Query (leader) PDB : 5BSR; Ligand: AMP; Similar sites found: 86
This union binding pocket(no: 2) in the query (biounit: 5bsr.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3R75 PYR 0.008512 0.44927 0.922509
2 2Z49 AMG 0.02832 0.41988 1.62037
3 2WW2 SWA 0.03163 0.42009 1.66052
4 2J3M ATP 0.01739 0.40089 1.66052
5 2ZWI C5P 0.03902 0.40786 2.68097
6 3NKS ACJ 0.02916 0.40451 2.72537
7 1RZU ADP 0.0283 0.41527 2.8866
8 1G27 BB1 0.0132 0.41496 2.97619
9 3JQ3 ADP 0.02516 0.41797 3.00546
10 4DS0 A2G GAL NAG FUC 0.001205 0.51241 3.06748
11 3OJI PYV 0.0195 0.40407 3.1746
12 2X1L ADN 0.04745 0.40684 3.43511
13 4YH2 GSH 0.01329 0.44127 3.6036
14 2H3H BGC 0.04749 0.40683 3.83387
15 3QPB R1P 0.03907 0.40783 3.90071
16 5KJW 53C 0.02824 0.42218 3.98126
17 4RI6 GSH 0.0123 0.43858 4.65116
18 1FHX 4IP 0.04255 0.40586 4.65116
19 5F05 GSH 0.03842 0.40822 4.71698
20 4PNG GSF 0.03161 0.41646 4.80349
21 5EGM 5NY 0.02274 0.40096 4.83871
22 2J5V RGP 0.01066 0.45126 4.90463
23 4EPM AMP 0.003844 0.42699 5.35055
24 3BPX SAL 0.03186 0.42231 5.40541
25 5FPE 3TR 0.01055 0.44378 6.45995
26 4Y4V DAL 0.03848 0.40307 6.64207
27 5JY4 ISC 0.02177 0.41079 6.90537
28 3QDU CBS CBS 0.04821 0.40968 6.99301
29 4B2G V1N 0.001634 0.44656 7.01107
30 3VWX GSH 0.02106 0.43023 7.20721
31 5B19 TLA 0.0393 0.41131 7.32759
32 2GN3 MAN 0.0461 0.4195 7.53968
33 5KOD AMP 0.0003522 0.50367 7.56458
34 1I7Q PYR 0.04152 0.40992 7.77202
35 5G3L SIA 0.0441 0.40339 8.08081
36 3BMN AX3 0.03909 0.4052 9.02778
37 3VY6 BGC BGC 0.03857 0.41894 9.21986
38 2PKA BEN 0.04518 0.41356 10
39 2UYQ SAM 0.01952 0.4364 10.3226
40 1O5E 132 0.02202 0.41384 10.5882
41 1NME 159 0.04645 0.40728 10.8696
42 1S17 GNR 0.01385 0.41397 11.1111
43 2NUO BGC 0.03004 0.42936 11.4754
44 2Y4N DLL 0.000002426 0.54123 12.5858
45 2Y4N PAC 0.00002308 0.53363 12.5858
46 3IWD M2T 0.02447 0.42365 14.5161
47 3N5O GSH 0.009055 0.42268 15.3191
48 4DG8 AMP 0.0000004986 0.63764 24.5387
49 5N9X ATP 0.0000005861 0.60565 25.3308
50 5N9X 8QN 0.0000004877 0.60282 25.3308
51 5N9X THR 0.0003388 0.53594 25.3308
52 4DR9 BB2 0.0255 0.4074 28.125
53 5MST AMP 0.0000002798 0.63431 30.2583
54 5MST FUM 0.0000005114 0.58985 30.2583
55 2Y4O DLL 0.0000002483 0.60941 33.1828
56 5D6J ATP 0.000003423 0.40821 33.9483
57 5HM3 649 0.000006956 0.51871 34.1328
58 5EY9 5SV 0.00001363 0.52422 34.3173
59 5OE4 3UK 0.00000004628 0.65542 35.1351
60 5MSD AMP 0.00000003308 0.69519 35.7934
61 5MSD BEZ 0.00000002385 0.67626 35.7934
62 4R0M FA5 0.00000005061 0.49183 35.7934
63 3NYQ MCA 0.0000001757 0.57163 37.0297
64 3NYQ AMP 0.0000001381 0.57079 37.0297
65 4GR5 APC 0.000001275 0.62546 37.4539
66 3E7W AMP 0.00001622 0.57037 38.9432
67 3DHV DAL AMP 0.0000006673 0.6031 40.4297
68 4OXI GAP 0.00000004874 0.46732 41.3284
69 4GXQ ATP 0.0000001619 0.63087 41.502
70 1AMU AMP 0.000001075 0.62135 41.5129
71 4D57 ARG AMP 0.00000001557 0.59613 41.6974
72 3O84 HTJ 0.000001011 0.57171 41.6974
73 5C5H 4YB 0.00000186 0.5555 41.7219
74 4FUT ATP 0.0000003867 0.6206 41.9483
75 1MDB AMP DBH 0.00000009748 0.64813 42.6716
76 3C5E ATP 0.000001326 0.46116 43.1734
77 3KXW 1ZZ 0.0000008174 0.57026 43.5424
78 1PG4 PRX 0.0000241 0.4495 43.7269
79 1PG4 COA 0.0000241 0.4495 43.7269
80 1V25 ANP 0.000000001097 0.64385 43.9926
81 4RLQ 3SK 0.000003514 0.49279 44.1233
82 3CW9 AMP 0.000001567 0.60611 47.619
83 3CW9 01A 0.003115 0.41947 47.619
84 2D1S SLU 0.00000007108 0.59708 49.4465
85 5IE3 OXD 0.00000003979 0.50486 49.6109
86 5IE3 AMP 0.00000003979 0.50486 49.6109
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