Receptor
PDB id Resolution Class Description Source Keywords
5BSW 2.1 Å EC: 6.2.1.12 CRYSTAL STRUCTURE OF 4-COUMARATE:COA LIGASE DELTA-V341 MUTAN COMPLEXED WITH FERULOYL 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
4UW A:600;
B:600;
Valid;
Valid;
none;
none;
submit data
523.39 C20 H22 N5 O10 P COC1=...
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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: 4UW; Similar ligands found: 227
No: Ligand ECFP6 Tc MDL keys Tc
1 4UW 1 1
2 4UU 0.752381 0.961039
3 4UV 0.700935 0.961039
4 CA0 0.626263 0.886076
5 5AL 0.621359 0.922078
6 A2D 0.591837 0.884615
7 PAJ 0.587156 0.855422
8 1ZZ 0.580357 0.857143
9 BA3 0.58 0.884615
10 SRP 0.579439 0.875
11 M33 0.578431 0.897436
12 8QN 0.577982 0.922078
13 B4P 0.574257 0.884615
14 ADP 0.574257 0.860759
15 AP5 0.574257 0.884615
16 ACP 0.572816 0.839506
17 4AD 0.572727 0.864198
18 AN2 0.568627 0.85
19 DLL 0.567568 0.922078
20 00A 0.567568 0.876543
21 PRX 0.567308 0.839506
22 TXA 0.566372 0.898734
23 PTJ 0.566372 0.865854
24 ANP 0.566038 0.839506
25 OOB 0.563636 0.922078
26 ADX 0.563107 0.781609
27 AMP 0.561224 0.858974
28 A 0.561224 0.858974
29 ABM 0.56 0.884615
30 AMO 0.558559 0.875
31 ATP 0.557692 0.860759
32 50T 0.557692 0.82716
33 WAQ 0.557522 0.853659
34 PR8 0.557522 0.823529
35 ME8 0.552632 0.857143
36 AR6 0.552381 0.884615
37 APR 0.552381 0.884615
38 5FA 0.552381 0.860759
39 AQP 0.552381 0.860759
40 ACQ 0.551402 0.839506
41 5SV 0.54955 0.821429
42 A12 0.54902 0.829268
43 AP2 0.54902 0.829268
44 3UK 0.548673 0.910256
45 AD9 0.54717 0.839506
46 SAP 0.54717 0.819277
47 AGS 0.54717 0.819277
48 LAD 0.54386 0.833333
49 ATF 0.541284 0.829268
50 AHX 0.539823 0.821429
51 NB8 0.53913 0.843373
52 3OD 0.53913 0.910256
53 SON 0.538462 0.875
54 LAQ 0.53719 0.813953
55 GAP 0.537037 0.8625
56 OAD 0.535088 0.910256
57 AMP MG 0.534653 0.814815
58 AU1 0.533333 0.839506
59 YLC 0.532258 0.857143
60 9SN 0.529915 0.865854
61 A22 0.526786 0.873418
62 FA5 0.525424 0.898734
63 YAP 0.525424 0.8875
64 SRA 0.524752 0.817073
65 APC 0.523364 0.829268
66 TAT 0.522936 0.829268
67 25A 0.522124 0.884615
68 YLP 0.520325 0.837209
69 ADV 0.518519 0.851852
70 RBY 0.518519 0.851852
71 A1R 0.517544 0.809524
72 ADQ 0.517544 0.886076
73 DAL AMP 0.513274 0.897436
74 G3A 0.512397 0.843373
75 IOT 0.511811 0.786517
76 MYR AMP 0.508475 0.835294
77 XAH 0.508333 0.793103
78 G5P 0.508197 0.843373
79 YLB 0.507937 0.816092
80 ADP MG 0.504673 0.82716
81 GTA 0.504065 0.857143
82 NAI 0.504 0.924051
83 TYM 0.5 0.898734
84 ADP BEF 0.5 0.807229
85 OMR 0.5 0.847059
86 BEF ADP 0.5 0.807229
87 BIS 0.5 0.809524
88 MAP 0.5 0.819277
89 48N 0.496 0.888889
90 25L 0.495798 0.873418
91 AYB 0.492308 0.806818
92 NAX 0.492063 0.890244
93 ADP PO3 0.490909 0.858974
94 FYA 0.487395 0.85
95 ATP MG 0.486486 0.82716
96 YLA 0.484615 0.816092
97 139 0.484615 0.845238
98 T5A 0.484615 0.880952
99 4TC 0.484375 0.865854
100 AP0 0.484375 0.9125
101 VO4 ADP 0.482456 0.85
102 ADP VO4 0.482456 0.85
103 BT5 0.481203 0.786517
104 CNA 0.480916 0.875
105 A4P 0.48062 0.818182
106 DND 0.480315 0.898734
107 NXX 0.480315 0.898734
108 UP5 0.480315 0.8875
109 TXD 0.480315 0.876543
110 6V0 0.480315 0.9125
111 YLY 0.477941 0.827586
112 TXE 0.476562 0.876543
113 ADP ALF 0.473684 0.797619
114 ALF ADP 0.473684 0.797619
115 UPA 0.472868 0.876543
116 LPA AMP 0.472441 0.793103
117 TYR AMP 0.471545 0.875
118 ADP BMA 0.470588 0.8625
119 ANP MG 0.469565 0.819277
120 TAD 0.468254 0.811765
121 A A 0.466667 0.860759
122 ATP A A A 0.463415 0.871795
123 JB6 0.46281 0.831325
124 NAD 0.462687 0.897436
125 COD 0.462687 0.769231
126 ADJ 0.462121 0.869048
127 A5A 0.46087 0.784091
128 AFH 0.460317 0.833333
129 5AS 0.458716 0.73913
130 N0B 0.457143 0.837209
131 M24 0.456522 0.845238
132 A3D 0.455882 0.910256
133 AHZ 0.453125 0.835294
134 VMS 0.452991 0.766667
135 52H 0.452991 0.758242
136 54H 0.452991 0.766667
137 G A A A 0.451852 0.821429
138 BTX 0.451852 0.775281
139 PAP 0.451327 0.848101
140 A3P 0.449541 0.858974
141 TSB 0.449153 0.775281
142 7MD 0.448819 0.813953
143 AOC 0.448598 0.772152
144 G5A 0.447368 0.73913
145 NAE 0.442857 0.8875
146 P5A 0.442623 0.708333
147 2A5 0.442478 0.795181
148 ARG AMP 0.44186 0.784091
149 EAD 0.440559 0.91358
150 5CD 0.44 0.734177
151 NAQ 0.439716 0.865854
152 PPS 0.439655 0.761364
153 7MC 0.439394 0.837209
154 RAB 0.438776 0.746835
155 XYA 0.438776 0.746835
156 ADN 0.438776 0.746835
157 ATR 0.438596 0.835443
158 DZD 0.437956 0.833333
159 U A G G 0.437956 0.831325
160 53H 0.436975 0.758242
161 ZID 0.43662 0.886076
162 NAD IBO 0.433824 0.864198
163 MTA 0.432692 0.75
164 FB0 0.432432 0.763441
165 SSA 0.432203 0.73913
166 5N5 0.43 0.725
167 LSS 0.429752 0.741935
168 DSZ 0.429752 0.758242
169 A2R 0.428571 0.873418
170 P1H 0.428571 0.891566
171 7D5 0.428571 0.780488
172 7D3 0.427273 0.783133
173 EP4 0.427184 0.731707
174 AR6 AR6 0.426357 0.884615
175 NVA LMS 0.42623 0.741935
176 6RE 0.425926 0.678161
177 A4D 0.425743 0.725
178 5CA 0.425 0.73913
179 7D4 0.424779 0.783133
180 ITT 0.424779 0.8125
181 3DH 0.424528 0.728395
182 6FA 0.423841 0.816092
183 A2P 0.423423 0.846154
184 DTA 0.423077 0.740741
185 M2T 0.423077 0.714286
186 NDC 0.422819 0.843373
187 LEU LMS 0.422764 0.741935
188 AMP DBH 0.421875 0.839506
189 AF3 ADP 3PG 0.421053 0.811765
190 LA8 ALF 3PG 0.421053 0.811765
191 ALF ADP 3PG 0.421053 0.811765
192 5X8 0.421053 0.740741
193 3AM 0.420561 0.822785
194 4TA 0.42029 0.869048
195 0WD 0.42029 0.9125
196 A3N 0.418182 0.719512
197 J7C 0.418182 0.686047
198 NSS 0.418033 0.73913
199 6AD 0.415254 0.833333
200 ARU 0.414634 0.770115
201 NA7 0.41129 0.829268
202 NAJ PYZ 0.409722 0.823529
203 FAD 0.409091 0.825581
204 SFD 0.409091 0.717172
205 FAS 0.409091 0.825581
206 NDP 0.408759 0.9125
207 SMM 0.408333 0.727273
208 GSU 0.408 0.758242
209 KAA 0.408 0.715789
210 FDA 0.407895 0.829545
211 7C5 0.407692 0.792683
212 FNK 0.407643 0.802198
213 AMP NAD 0.406897 0.898734
214 V3L 0.40678 0.884615
215 IMO 0.405405 0.822785
216 FAY 0.405063 0.835294
217 P5F 0.404908 0.820225
218 AAT 0.403361 0.689655
219 YSA 0.403101 0.758242
220 NJP 0.402878 0.864198
221 U G A 0.402597 0.813953
222 S4M 0.401786 0.67033
223 GJV 0.401786 0.670455
224 SA8 0.401709 0.729412
225 NAJ PZO 0.401408 0.888889
226 NDE 0.4 0.875
227 A A A 0.4 0.82716
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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