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 293 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 250 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 204 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: 202
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 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 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Ligand no: 2; Ligand: A1S; Similar ligands found: 147
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 COK 0.821705 0.955056
17 OXK 0.821705 0.955056
18 4CA 0.819549 0.966292
19 3HC 0.816794 0.965909
20 0T1 0.816 0.954545
21 COA 0.816 0.977012
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 BCO 0.80303 0.955056
30 MLC 0.80303 0.955056
31 1HE 0.80303 0.977528
32 0ET 0.80292 0.977528
33 ETB 0.8 0.921348
34 FAM 0.79845 0.933333
35 FCX 0.79845 0.923077
36 CAA 0.796992 0.965909
37 0FQ 0.79562 0.977273
38 4CO 0.79562 0.966292
39 MCD 0.793893 0.955056
40 NHW 0.791367 0.977528
41 NHM 0.791367 0.977528
42 UOQ 0.791367 0.977528
43 SCA 0.791045 0.955056
44 MC4 0.791045 0.904255
45 CMX 0.790698 0.954545
46 SCO 0.790698 0.954545
47 01A 0.789855 0.934783
48 BYC 0.785185 0.955056
49 COW 0.785185 0.944444
50 2KQ 0.785185 0.955556
51 1GZ 0.785185 0.944444
52 HGG 0.785185 0.955056
53 SCD 0.781955 0.954545
54 TGC 0.781022 0.966292
55 CA6 0.780303 0.90625
56 BCA 0.779412 0.944444
57 FAQ 0.779412 0.955056
58 HAX 0.778626 0.933333
59 HXC 0.773723 0.955556
60 GRA 0.773723 0.955056
61 HFQ 0.77305 0.955556
62 CAJ 0.768657 0.933333
63 NHQ 0.763889 0.988506
64 1CZ 0.76259 0.944444
65 CO8 0.76259 0.955556
66 2NE 0.76259 0.934066
67 NMX 0.761194 0.884211
68 MRS 0.760563 0.955556
69 MRR 0.760563 0.955556
70 01K 0.760274 0.977273
71 CS8 0.758865 0.966667
72 MYA 0.757143 0.955556
73 DCC 0.757143 0.955556
74 MFK 0.757143 0.955556
75 5F9 0.757143 0.955556
76 ST9 0.757143 0.955556
77 UCC 0.757143 0.955556
78 HDC 0.753521 0.955556
79 1CV 0.746479 0.955056
80 WCA 0.746479 0.934066
81 CA8 0.746377 0.867347
82 CA3 0.744966 0.977273
83 YE1 0.744526 0.94382
84 4KX 0.741259 0.923913
85 COT 0.731544 0.977273
86 DAK 0.731034 0.945055
87 YNC 0.731034 0.944444
88 93P 0.727273 0.966292
89 8Z2 0.726027 0.945055
90 1HA 0.718121 0.934066
91 S0N 0.713287 0.933333
92 CA5 0.698718 0.934783
93 F8G 0.697368 0.914894
94 93M 0.69375 0.966292
95 CCQ 0.689655 0.934783
96 7L1 0.686131 0.966292
97 UCA 0.672956 0.955556
98 CO7 0.671329 0.955056
99 COD 0.661654 0.965517
100 4BN 0.624277 0.914894
101 5TW 0.624277 0.914894
102 OXT 0.622093 0.914894
103 JBT 0.597765 0.895833
104 BSJ 0.591954 0.945055
105 ASP ASP ASP ILE CMC NH2 0.584337 0.933333
106 HMG 0.580645 0.922222
107 PLM COA 0.573248 0.923077
108 COA PLM 0.573248 0.923077
109 PAP 0.54918 0.793103
110 ACE SER ASP ALY THR NH2 COA 0.544444 0.933333
111 SFC 0.512048 0.934066
112 RFC 0.512048 0.934066
113 PPS 0.5 0.736842
114 A3P 0.5 0.781609
115 191 0.49375 0.848485
116 0WD 0.493243 0.771739
117 PTJ 0.442857 0.852273
118 3AM 0.439024 0.770115
119 A22 0.430657 0.795455
120 PUA 0.43038 0.802198
121 A2D 0.425197 0.784091
122 PAJ 0.42446 0.863636
123 48N 0.422819 0.791209
124 3OD 0.422535 0.806818
125 AGS 0.421053 0.788889
126 SAP 0.421053 0.788889
127 ATR 0.421053 0.781609
128 ADP 0.415385 0.804598
129 YLB 0.414474 0.88764
130 YLP 0.413333 0.866667
131 A2R 0.413043 0.795455
132 OAD 0.408451 0.806818
133 NA7 0.408451 0.83908
134 BA3 0.407692 0.784091
135 HEJ 0.406015 0.804598
136 ATP 0.406015 0.804598
137 B4P 0.40458 0.784091
138 AP5 0.40458 0.784091
139 APR 0.402985 0.784091
140 AQP 0.402985 0.804598
141 5FA 0.402985 0.804598
142 AR6 0.402985 0.784091
143 2A5 0.402985 0.827586
144 ME8 0.402778 0.865169
145 AN2 0.401515 0.795455
146 5AL 0.40146 0.795455
147 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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