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 319 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 271 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 223 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 (2D)
Ligand no: 1; Ligand: SAM; Similar ligands found: 246
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 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
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 EU9 0.537037 0.809524
21 DTA 0.536585 0.789474
22 62X 0.535354 0.884615
23 MTA 0.53012 0.875
24 3DH 0.517647 0.849315
25 AMP MG 0.517241 0.7375
26 5AL 0.510417 0.743902
27 VMS 0.510204 0.673913
28 54H 0.510204 0.673913
29 0UM 0.51 0.857143
30 NWW 0.506173 0.739726
31 LMS 0.505747 0.666667
32 AMP 0.505747 0.707317
33 A 0.505747 0.707317
34 45A 0.505618 0.753086
35 ABM 0.505618 0.753086
36 A5A 0.505155 0.688889
37 SSA 0.5 0.684783
38 5AD 0.5 0.75
39 SON 0.5 0.746988
40 6RE 0.5 0.78481
41 SRP 0.5 0.746988
42 K15 0.5 0.883117
43 LSS 0.49505 0.706522
44 CA0 0.494624 0.714286
45 AP2 0.494505 0.705882
46 A12 0.494505 0.705882
47 ME8 0.490385 0.841463
48 TSB 0.49 0.681319
49 5CA 0.49 0.684783
50 DAL AMP 0.49 0.765432
51 53H 0.49 0.666667
52 ACP 0.489362 0.694118
53 KG4 0.489362 0.714286
54 ADP 0.48913 0.690476
55 5AS 0.48913 0.648936
56 J7C 0.488889 0.772152
57 A2D 0.488889 0.690476
58 ZAS 0.488636 0.769231
59 8QN 0.485149 0.743902
60 9ZD 0.485149 0.729412
61 9ZA 0.485149 0.729412
62 8LH 0.484848 0.746988
63 GAP 0.484536 0.73494
64 AN2 0.483871 0.682353
65 A3S 0.483871 0.813333
66 ADP BEF 0.483871 0.728395
67 ADP MG 0.483871 0.728395
68 A7D 0.483871 0.851351
69 GJV 0.483516 0.775
70 SRA 0.483146 0.694118
71 GSU 0.480769 0.722222
72 KAA 0.480769 0.698925
73 LAD 0.480769 0.752941
74 DSZ 0.480392 0.703297
75 AMO 0.480392 0.746988
76 52H 0.48 0.666667
77 8LE 0.479592 0.717647
78 APC MG 0.479167 0.731707
79 M33 0.478723 0.722892
80 BA3 0.478261 0.690476
81 MAO 0.478261 0.82716
82 AOC 0.477778 0.776316
83 NEC 0.477778 0.75
84 DSH 0.477778 0.842105
85 SXZ 0.47619 0.894737
86 NVA LMS 0.475728 0.736264
87 AHX 0.475728 0.701149
88 Y3J 0.47561 0.706667
89 8LQ 0.475248 0.768293
90 QA7 0.475248 0.738095
91 G5A 0.474227 0.684783
92 A3T 0.473684 0.8
93 B4P 0.473118 0.690476
94 AP5 0.473118 0.690476
95 A3N 0.472527 0.766234
96 KB1 0.471698 0.833333
97 LEU LMS 0.471154 0.752809
98 PRX 0.46875 0.73494
99 APC 0.46875 0.705882
100 AT4 0.468085 0.686047
101 4AD 0.466019 0.759036
102 PAJ 0.466019 0.712644
103 NWQ 0.465909 0.767123
104 V2G 0.464646 0.701149
105 ATP MG 0.463918 0.728395
106 ADP PO3 0.463918 0.728395
107 ADV 0.463918 0.72619
108 RBY 0.463918 0.72619
109 ADX 0.463158 0.666667
110 MHZ 0.463158 0.82716
111 AU1 0.463158 0.674419
112 NB8 0.462264 0.72093
113 TXA 0.462264 0.72619
114 A3G 0.461538 0.802632
115 ANP MG 0.46 0.702381
116 VO4 ADP 0.46 0.694118
117 BEF ADP 0.459184 0.710843
118 VRT 0.459184 0.842105
119 XAH 0.458716 0.715909
120 KYE 0.458716 0.802469
121 YSA 0.458716 0.684783
122 50T 0.458333 0.682353
123 ATP 0.458333 0.690476
124 H1Q 0.458333 0.719512
125 HEJ 0.458333 0.690476
126 7D7 0.45679 0.723684
127 V47 0.455446 0.810811
128 KH3 0.455357 0.871795
129 ACQ 0.454545 0.694118
130 AR6 0.453608 0.710843
131 APR 0.453608 0.710843
132 5FA 0.453608 0.690476
133 AQP 0.453608 0.690476
134 NSS 0.451923 0.703297
135 FA5 0.449541 0.746988
136 AGS 0.44898 0.678161
137 A5D 0.44898 0.789474
138 AD9 0.44898 0.674419
139 PTJ 0.448598 0.72093
140 YLB 0.448276 0.758621
141 YLP 0.447368 0.738636
142 OZP 0.447368 0.844156
143 8X1 0.446602 0.680851
144 D3Y 0.446602 0.792208
145 N5O 0.445652 0.789474
146 ALF ADP 0.445545 0.678161
147 3AM 0.444444 0.674699
148 MYR AMP 0.444444 0.776471
149 HY8 0.443478 0.822785
150 OAD 0.443396 0.73494
151 2VA 0.443299 0.779221
152 KXW 0.442478 0.844156
153 QXP 0.442308 0.67033
154 S8M 0.442308 0.831169
155 OOB 0.442308 0.722892
156 6YZ 0.441176 0.694118
157 T99 0.44 0.686047
158 ANP 0.44 0.674419
159 TAT 0.44 0.686047
160 N37 0.439655 0.828947
161 WAQ 0.439252 0.75
162 HZ2 0.438596 0.822785
163 8PZ 0.436364 0.684783
164 B5Y 0.436364 0.717647
165 N5A 0.43617 0.786667
166 F0P 0.435897 0.844156
167 YLC 0.435897 0.755814
168 AAT 0.435644 0.797468
169 1ZZ 0.435185 0.755814
170 3OD 0.435185 0.73494
171 9K8 0.435185 0.663158
172 NVA 2AD 0.434343 0.855263
173 00A 0.433962 0.689655
174 DLL 0.433962 0.722892
175 7MD 0.433628 0.715909
176 ARG AMP 0.433628 0.727273
177 ATF 0.431373 0.666667
178 SO8 0.43 0.792208
179 A6D 0.429907 0.72619
180 QXG 0.429907 0.663043
181 9X8 0.429907 0.717647
182 3UK 0.429907 0.714286
183 F2R 0.429752 0.7
184 OZV 0.428571 0.690476
185 AMP DBH 0.428571 0.714286
186 5SV 0.428571 0.741176
187 TYM 0.42735 0.746988
188 WSA 0.42735 0.692308
189 9SN 0.427273 0.681818
190 AHZ 0.426087 0.755814
191 PR8 0.425926 0.744186
192 B5V 0.425926 0.705882
193 J4G 0.425926 0.759036
194 3NZ 0.425926 0.807692
195 P5A 0.425926 0.691489
196 R2V 0.425926 0.67033
197 A1R 0.424528 0.709302
198 2A5 0.424242 0.674419
199 Q34 0.423729 0.802469
200 7MC 0.423729 0.719101
201 Q2M 0.423729 0.846154
202 B5M 0.423423 0.717647
203 HQG 0.423077 0.702381
204 U4Y 0.422414 0.88
205 7D5 0.422222 0.658824
206 JB6 0.422018 0.709302
207 FYA 0.422018 0.722892
208 AYB 0.421488 0.75
209 JNT 0.420561 0.694118
210 K2H 0.420561 0.805195
211 B1U 0.419643 0.632653
212 MAP 0.419048 0.659091
213 KY2 0.419048 0.777778
214 A22 0.419048 0.682353
215 2AM 0.417582 0.666667
216 TAD 0.417391 0.712644
217 ADP BMA 0.416667 0.714286
218 A3P 0.416667 0.686747
219 25A 0.415094 0.690476
220 Q2V 0.413223 0.833333
221 YLA 0.413223 0.719101
222 K2K 0.412844 0.807692
223 8Q2 0.411765 0.663158
224 KYB 0.411215 0.777778
225 A3R 0.411215 0.709302
226 ADQ 0.411215 0.694118
227 KMQ 0.410714 0.72619
228 48N 0.410256 0.72093
229 0XU 0.41 0.824324
230 GA7 0.408696 0.72619
231 K3H 0.40708 0.775
232 7D3 0.40625 0.643678
233 PAP 0.405941 0.678571
234 DQV 0.405172 0.702381
235 OVE 0.404255 0.662791
236 4UV 0.403509 0.697674
237 ALF ADP 3PG 0.403361 0.712644
238 AF3 ADP 3PG 0.403361 0.712644
239 Q2P 0.403226 0.802469
240 3AD 0.402299 0.783784
241 2BA 0.402062 0.682927
242 CMP 0.402062 0.691358
243 K38 0.401786 0.7375
244 NAD TDB 0.4 0.731707
245 7C5 0.4 0.731707
246 NAD IBO 0.4 0.731707
Ligand no: 2; Ligand: A1S; Similar ligands found: 175
No: Ligand ECFP6 Tc MDL keys Tc
1 A1S 1 1
2 SOP 0.865079 0.977273
3 CMC 0.858268 0.977273
4 CAO 0.854839 0.944444
5 COS 0.854839 0.955056
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 3KK 0.828125 0.955056
13 FYN 0.828125 0.977012
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 AMX 0.811024 0.965517
26 30N 0.811024 0.894737
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 BCO 0.80303 0.955056
32 MLC 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 NHM 0.791367 0.977528
44 NHW 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 HGG 0.785185 0.955056
51 KFV 0.785185 0.876289
52 BYC 0.785185 0.955056
53 2KQ 0.785185 0.955556
54 1GZ 0.785185 0.944444
55 COW 0.785185 0.944444
56 SCD 0.781955 0.954545
57 TGC 0.781022 0.966292
58 YZS 0.780303 0.867347
59 KGP 0.780303 0.867347
60 CA6 0.780303 0.90625
61 BCA 0.779412 0.944444
62 FAQ 0.779412 0.955056
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 CO8 0.76259 0.955556
70 2NE 0.76259 0.934066
71 1CZ 0.76259 0.944444
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 LCV 0.757353 0.858586
78 SO5 0.757353 0.858586
79 ST9 0.757143 0.955556
80 5F9 0.757143 0.955556
81 DCC 0.757143 0.955556
82 MYA 0.757143 0.955556
83 UCC 0.757143 0.955556
84 MFK 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 DAK 0.731034 0.945055
97 YNC 0.731034 0.944444
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 RMW 0.687898 0.934066
107 7L1 0.686131 0.966292
108 UCA 0.672956 0.955556
109 CO7 0.671329 0.955056
110 COD 0.661654 0.965517
111 N9V 0.644295 0.902174
112 4BN 0.624277 0.914894
113 5TW 0.624277 0.914894
114 OXT 0.622093 0.914894
115 COA FLC 0.605634 0.943182
116 BUA COA 0.604027 0.922222
117 JBT 0.597765 0.895833
118 BSJ 0.591954 0.945055
119 6NA COA 0.584416 0.923077
120 ASP ASP ASP ILE NH2 CMC 0.584337 0.933333
121 HMG 0.580645 0.922222
122 DKA COA 0.573248 0.923077
123 MYR COA 0.573248 0.923077
124 DCR COA 0.573248 0.923077
125 PLM COA 0.573248 0.923077
126 DAO COA 0.573248 0.923077
127 EO3 COA 0.573248 0.923077
128 X90 COA 0.573248 0.923077
129 PAP 0.54918 0.793103
130 ACE SER ASP ALY THR NH2 COA 0.544444 0.933333
131 MET VAL ASN ALA CMC 0.533333 0.955056
132 SFC 0.512048 0.934066
133 RFC 0.512048 0.934066
134 A3P 0.5 0.781609
135 PPS 0.5 0.736842
136 ACE MET LEU GLY PRO NH2 COA 0.497409 0.955056
137 0WD 0.493243 0.771739
138 5AD NJS 0.463277 0.893617
139 PTJ 0.442857 0.852273
140 3AM 0.439024 0.770115
141 A22 0.430657 0.795455
142 QA7 0.430657 0.829545
143 PUA 0.43038 0.802198
144 UBG 0.427746 0.826087
145 A2D 0.425197 0.784091
146 PAJ 0.42446 0.863636
147 HQG 0.423358 0.795455
148 48N 0.422819 0.791209
149 3OD 0.422535 0.806818
150 AGS 0.421053 0.788889
151 ATR 0.421053 0.781609
152 9BG 0.419355 0.771739
153 ADP 0.415385 0.804598
154 YLB 0.414474 0.88764
155 YLP 0.413333 0.866667
156 A2R 0.413043 0.795455
157 8LE 0.411765 0.829545
158 8LQ 0.410072 0.818182
159 OAD 0.408451 0.806818
160 NA7 0.408451 0.83908
161 BA3 0.407692 0.784091
162 HEJ 0.406015 0.804598
163 ATP 0.406015 0.804598
164 AP5 0.40458 0.784091
165 B4P 0.40458 0.784091
166 APR 0.402985 0.784091
167 AQP 0.402985 0.804598
168 2A5 0.402985 0.827586
169 5FA 0.402985 0.804598
170 AR6 0.402985 0.784091
171 ME8 0.402778 0.865169
172 AN2 0.401515 0.795455
173 5AL 0.40146 0.795455
174 JNT 0.401408 0.827586
175 F2R 0.401274 0.846154
Similar Ligands (3D)
Ligand no: 1; Ligand: SAM; Similar ligands found: 26
No: Ligand Similarity coefficient
1 TT8 0.9650
2 GDP 0.9145
3 8OD 0.9006
4 NWZ 0.8954
5 IDP 0.8910
6 CUU 0.8833
7 GNH 0.8826
8 KB7 0.8802
9 DTP 0.8779
10 GDP MG 0.8767
11 M7G 0.8755
12 G8D 0.8722
13 DZ4 0.8710
14 GTP 0.8703
15 DAT 0.8676
16 DGT 0.8665
17 GNP 0.8658
18 AV2 0.8650
19 HF7 0.8632
20 DGI 0.8627
21 HDV 0.8586
22 GCP 0.8586
23 TTP 0.8585
24 FZT 0.8567
25 GSP 0.8566
26 CTP 0.8538
Ligand no: 2; Ligand: A1S; Similar ligands found: 0
No: Ligand Similarity coefficient
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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