Receptor
PDB id Resolution Class Description Source Keywords
5W8A 2 Å EC: 7.-.-.- THE STRUCTURE OF A COA-DEPENDENT ACYL-HOMOSERINE LACTONE SYN BJAI, WITH SAM AND ISOPENTYL-COA BRADYRHIZOBIUM JAPONICUM ACYL-HOMOSERINE LACTONE COENZYME A BJAI BIOSYNTHETIC PROT
Ref.: MOLECULAR BASIS FOR THE SUBSTRATE SPECIFICITY OF QU SIGNAL SYNTHASES. PROC. NATL. ACAD. SCI. V. 114 9092 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:300;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
A1S A:301;
Valid;
none;
submit data
837.667 C26 H46 N7 O16 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W8E 1.8 Å EC: 7.-.-.- THE STRUCTURE OF A COA-DEPENDENT ACYL-HOMOSERINE LACTONE SYN BJAI, WITH THE ADDUCT OF SAH AND IV-COA BRADYRHIZOBIUM JAPONICUM ACYL-HOMOSERINE LACTONE COENZYME A BJAI BIOSYNTHETIC PROT
Ref.: MOLECULAR BASIS FOR THE SUBSTRATE SPECIFICITY OF QU SIGNAL SYNTHASES. PROC. NATL. ACAD. SCI. V. 114 9092 2017 U.S.A.
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 5W8A - A1S C26 H46 N7 O16 P3 S CC(C)CCSCC....
2 5W8G - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 5W8C - MTA C11 H15 N5 O3 S CSC[C@@H]1....
4 5W8E - SXZ C19 H28 N6 O6 S CC(C)CC(=O....
5 5W8D - MTA C11 H15 N5 O3 S CSC[C@@H]1....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5W8A - A1S C26 H46 N7 O16 P3 S CC(C)CCSCC....
2 5W8G - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 5W8C - MTA C11 H15 N5 O3 S CSC[C@@H]1....
4 5W8E - SXZ C19 H28 N6 O6 S CC(C)CC(=O....
5 5W8D - MTA C11 H15 N5 O3 S CSC[C@@H]1....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 5W8A - A1S C26 H46 N7 O16 P3 S CC(C)CCSCC....
2 5W8G - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 5W8C - MTA C11 H15 N5 O3 S CSC[C@@H]1....
4 5W8E - SXZ C19 H28 N6 O6 S CC(C)CC(=O....
5 5W8D - MTA C11 H15 N5 O3 S CSC[C@@H]1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 221
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 XYA 0.565789 0.773333
9 RAB 0.565789 0.773333
10 ADN 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 5X8 0.555556 0.888889
15 SFG 0.555556 0.875
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 5AL 0.510417 0.743902
25 VMS 0.510204 0.673913
26 54H 0.510204 0.673913
27 0UM 0.51 0.857143
28 A 0.505747 0.707317
29 AMP 0.505747 0.707317
30 LMS 0.505747 0.666667
31 ABM 0.505618 0.753086
32 45A 0.505618 0.753086
33 A5A 0.505155 0.688889
34 SRP 0.5 0.746988
35 K15 0.5 0.883117
36 SON 0.5 0.746988
37 6RE 0.5 0.78481
38 SSA 0.5 0.684783
39 5AD 0.5 0.75
40 LSS 0.49505 0.706522
41 CA0 0.494624 0.714286
42 A12 0.494505 0.705882
43 AP2 0.494505 0.705882
44 ME8 0.490385 0.841463
45 53H 0.49 0.666667
46 5CA 0.49 0.684783
47 DAL AMP 0.49 0.765432
48 TSB 0.49 0.681319
49 ACP 0.489362 0.694118
50 KG4 0.489362 0.714286
51 5AS 0.48913 0.648936
52 ADP 0.48913 0.690476
53 J7C 0.488889 0.772152
54 A2D 0.488889 0.690476
55 ZAS 0.488636 0.769231
56 9ZA 0.485149 0.729412
57 9ZD 0.485149 0.729412
58 8QN 0.485149 0.743902
59 8LH 0.484848 0.746988
60 GAP 0.484536 0.73494
61 AN2 0.483871 0.682353
62 ADP MG 0.483871 0.728395
63 A7D 0.483871 0.851351
64 A3S 0.483871 0.813333
65 GJV 0.483516 0.775
66 SRA 0.483146 0.694118
67 KAA 0.480769 0.698925
68 LAD 0.480769 0.752941
69 GSU 0.480769 0.722222
70 DSZ 0.480392 0.703297
71 AMO 0.480392 0.746988
72 52H 0.48 0.666667
73 8LE 0.479592 0.717647
74 APC MG 0.479167 0.731707
75 M33 0.478723 0.722892
76 MAO 0.478261 0.82716
77 BA3 0.478261 0.690476
78 AOC 0.477778 0.776316
79 NEC 0.477778 0.75
80 DSH 0.477778 0.842105
81 SXZ 0.47619 0.894737
82 AHX 0.475728 0.701149
83 NVA LMS 0.475728 0.736264
84 Y3J 0.47561 0.706667
85 8LQ 0.475248 0.768293
86 G5A 0.474227 0.684783
87 A3T 0.473684 0.8
88 AP5 0.473118 0.690476
89 B4P 0.473118 0.690476
90 A3N 0.472527 0.766234
91 KB1 0.471698 0.833333
92 APC 0.46875 0.705882
93 PRX 0.46875 0.73494
94 AT4 0.468085 0.686047
95 PAJ 0.466019 0.712644
96 4AD 0.466019 0.759036
97 ADP PO3 0.463918 0.728395
98 RBY 0.463918 0.72619
99 ADV 0.463918 0.72619
100 ATP MG 0.463918 0.728395
101 MHZ 0.463158 0.82716
102 ADX 0.463158 0.666667
103 AU1 0.463158 0.674419
104 YAP 0.462963 0.738095
105 TXA 0.462264 0.72619
106 NB8 0.462264 0.72093
107 A3G 0.461538 0.802632
108 VRT 0.459184 0.842105
109 YSA 0.458716 0.684783
110 XAH 0.458716 0.715909
111 H1Q 0.458333 0.719512
112 50T 0.458333 0.682353
113 HEJ 0.458333 0.690476
114 ATP 0.458333 0.690476
115 LEU LMS 0.457143 0.717391
116 7D7 0.45679 0.723684
117 KH3 0.455357 0.871795
118 ACQ 0.454545 0.694118
119 AQP 0.453608 0.690476
120 AR6 0.453608 0.710843
121 5FA 0.453608 0.690476
122 APR 0.453608 0.710843
123 NSS 0.451923 0.703297
124 FA5 0.449541 0.746988
125 A5D 0.44898 0.789474
126 AGS 0.44898 0.678161
127 SAP 0.44898 0.678161
128 AD9 0.44898 0.674419
129 PTJ 0.448598 0.72093
130 YLB 0.448276 0.758621
131 YLP 0.447368 0.738636
132 OZP 0.447368 0.844156
133 8X1 0.446602 0.680851
134 D3Y 0.446602 0.792208
135 N5O 0.445652 0.789474
136 ADP ALF 0.445545 0.678161
137 ALF ADP 0.445545 0.678161
138 MYR AMP 0.444444 0.776471
139 3AM 0.444444 0.674699
140 HY8 0.443478 0.822785
141 OAD 0.443396 0.73494
142 2VA 0.443299 0.779221
143 OOB 0.442308 0.722892
144 S8M 0.442308 0.831169
145 TYR AMP 0.441441 0.759036
146 6YZ 0.441176 0.694118
147 VO4 ADP 0.441176 0.702381
148 ADP VO4 0.441176 0.702381
149 ANP 0.44 0.674419
150 T99 0.44 0.686047
151 TAT 0.44 0.686047
152 N37 0.439655 0.828947
153 WAQ 0.439252 0.75
154 HZ2 0.438596 0.822785
155 8PZ 0.436364 0.684783
156 B5Y 0.436364 0.717647
157 N5A 0.43617 0.786667
158 F0P 0.435897 0.844156
159 YLC 0.435897 0.755814
160 AAT 0.435644 0.797468
161 1ZZ 0.435185 0.755814
162 9K8 0.435185 0.663158
163 3OD 0.435185 0.73494
164 NVA 2AD 0.434343 0.855263
165 00A 0.433962 0.689655
166 DLL 0.433962 0.722892
167 ARG AMP 0.433628 0.727273
168 7MD 0.433628 0.715909
169 ATF 0.431373 0.666667
170 SO8 0.43 0.792208
171 3UK 0.429907 0.714286
172 A6D 0.429907 0.72619
173 9X8 0.429907 0.717647
174 F2R 0.429752 0.7
175 AMP DBH 0.428571 0.714286
176 5SV 0.428571 0.741176
177 OZV 0.428571 0.690476
178 TYM 0.42735 0.746988
179 WSA 0.42735 0.692308
180 9SN 0.427273 0.681818
181 AHZ 0.426087 0.755814
182 P5A 0.425926 0.691489
183 J4G 0.425926 0.759036
184 PR8 0.425926 0.744186
185 A A 0.425926 0.710843
186 3NZ 0.425926 0.807692
187 B5V 0.425926 0.705882
188 A1R 0.424528 0.709302
189 2A5 0.424242 0.674419
190 7MC 0.423729 0.719101
191 B5M 0.423423 0.717647
192 HQG 0.423077 0.702381
193 7D5 0.422222 0.658824
194 JB6 0.422018 0.709302
195 FYA 0.422018 0.722892
196 AYB 0.421488 0.75
197 B1U 0.419643 0.632653
198 A22 0.419048 0.682353
199 MAP 0.419048 0.659091
200 2AM 0.417582 0.666667
201 TAD 0.417391 0.712644
202 ADP BMA 0.416667 0.714286
203 A3P 0.416667 0.686747
204 25A 0.415094 0.690476
205 YLA 0.413223 0.719101
206 8Q2 0.411765 0.663158
207 ADQ 0.411215 0.694118
208 A3R 0.411215 0.709302
209 48N 0.410256 0.72093
210 0XU 0.41 0.824324
211 GA7 0.408696 0.72619
212 7D3 0.40625 0.643678
213 PAP 0.405941 0.678571
214 DQV 0.405172 0.702381
215 OVE 0.404255 0.662791
216 4UV 0.403509 0.697674
217 AF3 ADP 3PG 0.403361 0.712644
218 3AD 0.402299 0.783784
219 CMP 0.402062 0.691358
220 2BA 0.402062 0.682927
221 7C5 0.4 0.731707
Ligand no: 2; Ligand: A1S; Similar ligands found: 163
No: Ligand ECFP6 Tc MDL keys Tc
1 A1S 1 1
2 SOP 0.865079 0.977273
3 CMC 0.858268 0.977273
4 COS 0.854839 0.955056
5 CAO 0.854839 0.944444
6 3CP 0.853846 0.977273
7 2CP 0.846154 0.966292
8 ACO 0.84127 0.966292
9 IVC 0.830769 0.965909
10 CO6 0.829457 0.955056
11 CIC 0.828358 0.977273
12 FYN 0.828125 0.977012
13 3KK 0.828125 0.955056
14 COF 0.825758 0.955556
15 MCA 0.824427 0.944444
16 OXK 0.821705 0.955056
17 COK 0.821705 0.955056
18 4CA 0.819549 0.966292
19 3HC 0.816794 0.965909
20 COA 0.816 0.977012
21 0T1 0.816 0.954545
22 1VU 0.815385 0.944444
23 DCA 0.814516 0.932584
24 IRC 0.81203 0.965909
25 30N 0.811024 0.894737
26 AMX 0.811024 0.965517
27 COO 0.810606 0.955056
28 2MC 0.80916 0.913979
29 YXS 0.804511 0.867347
30 YXR 0.804511 0.867347
31 MLC 0.80303 0.955056
32 BCO 0.80303 0.955056
33 1HE 0.80303 0.977528
34 0ET 0.80292 0.977528
35 ETB 0.8 0.921348
36 FCX 0.79845 0.923077
37 FAM 0.79845 0.933333
38 CAA 0.796992 0.965909
39 0FQ 0.79562 0.977273
40 4CO 0.79562 0.966292
41 MCD 0.793893 0.955056
42 UOQ 0.791367 0.977528
43 NHW 0.791367 0.977528
44 NHM 0.791367 0.977528
45 SCA 0.791045 0.955056
46 MC4 0.791045 0.904255
47 SCO 0.790698 0.954545
48 CMX 0.790698 0.954545
49 01A 0.789855 0.934783
50 1GZ 0.785185 0.944444
51 KFV 0.785185 0.876289
52 HGG 0.785185 0.955056
53 BYC 0.785185 0.955056
54 2KQ 0.785185 0.955556
55 COW 0.785185 0.944444
56 SCD 0.781955 0.954545
57 TGC 0.781022 0.966292
58 CA6 0.780303 0.90625
59 YZS 0.780303 0.867347
60 KGP 0.780303 0.867347
61 FAQ 0.779412 0.955056
62 BCA 0.779412 0.944444
63 HAX 0.778626 0.933333
64 HXC 0.773723 0.955556
65 GRA 0.773723 0.955056
66 HFQ 0.77305 0.955556
67 CAJ 0.768657 0.933333
68 NHQ 0.763889 0.988506
69 2NE 0.76259 0.934066
70 1CZ 0.76259 0.944444
71 CO8 0.76259 0.955556
72 NMX 0.761194 0.884211
73 MRS 0.760563 0.955556
74 MRR 0.760563 0.955556
75 01K 0.760274 0.977273
76 CS8 0.758865 0.966667
77 SO5 0.757353 0.858586
78 LCV 0.757353 0.858586
79 DCC 0.757143 0.955556
80 MFK 0.757143 0.955556
81 5F9 0.757143 0.955556
82 MYA 0.757143 0.955556
83 UCC 0.757143 0.955556
84 ST9 0.757143 0.955556
85 HDC 0.753521 0.955556
86 KGJ 0.75 0.875
87 WCA 0.746479 0.934066
88 1CV 0.746479 0.955056
89 CA8 0.746377 0.867347
90 CA3 0.744966 0.977273
91 YE1 0.744526 0.94382
92 J5H 0.743056 0.955056
93 4KX 0.741259 0.923913
94 KGA 0.733813 0.865979
95 COT 0.731544 0.977273
96 YNC 0.731034 0.944444
97 DAK 0.731034 0.945055
98 93P 0.727273 0.966292
99 8Z2 0.726027 0.945055
100 1HA 0.718121 0.934066
101 S0N 0.713287 0.933333
102 CA5 0.698718 0.934783
103 F8G 0.697368 0.914894
104 93M 0.69375 0.966292
105 CCQ 0.689655 0.934783
106 7L1 0.686131 0.966292
107 UCA 0.672956 0.955556
108 CO7 0.671329 0.955056
109 COD 0.661654 0.965517
110 N9V 0.644295 0.902174
111 5TW 0.624277 0.914894
112 4BN 0.624277 0.914894
113 OXT 0.622093 0.914894
114 COA FLC 0.605634 0.943182
115 JBT 0.597765 0.895833
116 BSJ 0.591954 0.945055
117 ASP ASP ASP ILE CMC NH2 0.584337 0.933333
118 HMG 0.580645 0.922222
119 PLM COA 0.573248 0.923077
120 COA PLM 0.573248 0.923077
121 PAP 0.54918 0.793103
122 ACE SER ASP ALY THR NH2 COA 0.544444 0.933333
123 RFC 0.512048 0.934066
124 SFC 0.512048 0.934066
125 A3P 0.5 0.781609
126 PPS 0.5 0.736842
127 191 0.49375 0.848485
128 0WD 0.493243 0.771739
129 PTJ 0.442857 0.852273
130 3AM 0.439024 0.770115
131 A22 0.430657 0.795455
132 PUA 0.43038 0.802198
133 A2D 0.425197 0.784091
134 PAJ 0.42446 0.863636
135 HQG 0.423358 0.795455
136 48N 0.422819 0.791209
137 3OD 0.422535 0.806818
138 SAP 0.421053 0.788889
139 ATR 0.421053 0.781609
140 AGS 0.421053 0.788889
141 9BG 0.419355 0.771739
142 ADP 0.415385 0.804598
143 YLB 0.414474 0.88764
144 YLP 0.413333 0.866667
145 A2R 0.413043 0.795455
146 8LE 0.411765 0.829545
147 8LQ 0.410072 0.818182
148 OAD 0.408451 0.806818
149 NA7 0.408451 0.83908
150 BA3 0.407692 0.784091
151 ATP 0.406015 0.804598
152 HEJ 0.406015 0.804598
153 B4P 0.40458 0.784091
154 AP5 0.40458 0.784091
155 2A5 0.402985 0.827586
156 APR 0.402985 0.784091
157 AQP 0.402985 0.804598
158 5FA 0.402985 0.804598
159 AR6 0.402985 0.784091
160 ME8 0.402778 0.865169
161 AN2 0.401515 0.795455
162 5AL 0.40146 0.795455
163 F2R 0.401274 0.846154
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W8E; Ligand: SXZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5w8e.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5W8E; Ligand: ADE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5w8e.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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