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 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....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 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 181 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: 192
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 ADN 0.565789 0.773333
10 RAB 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 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Ligand no: 2; Ligand: A1S; Similar ligands found: 143
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 AMX 0.811024 0.965517
26 30N 0.811024 0.894737
27 COO 0.810606 0.955056
28 2MC 0.80916 0.913979
29 BCO 0.80303 0.955056
30 1HE 0.80303 0.977528
31 MLC 0.80303 0.955056
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 NHM 0.791367 0.977528
41 NHW 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 1GZ 0.785185 0.944444
49 HGG 0.785185 0.955056
50 COW 0.785185 0.944444
51 BYC 0.785185 0.955056
52 2KQ 0.785185 0.955556
53 SCD 0.781955 0.954545
54 TGC 0.781022 0.966292
55 CA6 0.780303 0.90625
56 FAQ 0.779412 0.955056
57 BCA 0.779412 0.944444
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 2NE 0.76259 0.934066
65 1CZ 0.76259 0.944444
66 CO8 0.76259 0.955556
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 UCC 0.757143 0.955556
73 MFK 0.757143 0.955556
74 DCC 0.757143 0.955556
75 ST9 0.757143 0.955556
76 5F9 0.757143 0.955556
77 MYA 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 YNC 0.731034 0.944444
87 DAK 0.731034 0.945055
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 93M 0.69375 0.966292
94 CCQ 0.689655 0.934783
95 UCA 0.672956 0.955556
96 CO7 0.671329 0.955056
97 COD 0.661654 0.965517
98 4BN 0.624277 0.914894
99 5TW 0.624277 0.914894
100 OXT 0.622093 0.914894
101 JBT 0.597765 0.895833
102 BSJ 0.591954 0.945055
103 HMG 0.580645 0.922222
104 PLM COA 0.573248 0.923077
105 COA PLM 0.573248 0.923077
106 COA MYR 0.573248 0.923077
107 PAP 0.54918 0.793103
108 ACE SER ASP ALY THR NH2 COA 0.538043 0.933333
109 RFC 0.512048 0.934066
110 SFC 0.512048 0.934066
111 PPS 0.5 0.736842
112 A3P 0.5 0.781609
113 191 0.49375 0.848485
114 0WD 0.493243 0.771739
115 PTJ 0.442857 0.852273
116 3AM 0.439024 0.770115
117 A22 0.430657 0.795455
118 PUA 0.43038 0.802198
119 A2D 0.425197 0.784091
120 PAJ 0.42446 0.863636
121 48N 0.422819 0.791209
122 3OD 0.422535 0.806818
123 SAP 0.421053 0.788889
124 AGS 0.421053 0.788889
125 ATR 0.421053 0.781609
126 ADP 0.415385 0.804598
127 YLB 0.414474 0.88764
128 YLP 0.413333 0.866667
129 A2R 0.413043 0.795455
130 NA7 0.408451 0.83908
131 OAD 0.408451 0.806818
132 BA3 0.407692 0.784091
133 ATP 0.406015 0.804598
134 AP5 0.40458 0.784091
135 B4P 0.40458 0.784091
136 AQP 0.402985 0.804598
137 2A5 0.402985 0.827586
138 APR 0.402985 0.784091
139 5FA 0.402985 0.804598
140 AR6 0.402985 0.784091
141 ME8 0.402778 0.865169
142 AN2 0.401515 0.795455
143 5AL 0.40146 0.795455
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W8E; Ligand: SXZ; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 5w8e.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QSR ACO 0.0001496 0.47385 None
2 1QSN COA 0.0007689 0.46336 None
3 1Q2D COA 0.001287 0.45728 None
4 2JDC CAO 0.0008072 0.43373 None
5 1OJZ NAD 0.00518 0.42904 None
6 4KBA 1QM 0.04175 0.40236 1.80995
7 4U9W COA 0.006473 0.4058 1.93237
8 1CJW COT 0.0001349 0.43069 2.40964
9 1P0H COA 0.004242 0.41685 2.71493
10 1P0H ACO 0.004413 0.41685 2.71493
11 2ZFN ACO 0.005933 0.40738 3.16742
12 5FVJ ACO 0.001352 0.42785 3.61446
13 5K04 COA 0.01032 0.40274 3.61991
14 2WPX ACO 0.01667 0.40216 3.61991
15 1I1D 16G 0.001137 0.40896 3.72671
16 1I1D COA 0.000359 0.40183 3.72671
17 1KZL CRM 0.03121 0.40534 3.84615
18 4H6U ACO 0.007359 0.41209 4
19 4UWJ 7L5 0.0002271 0.46808 4.0724
20 4UWJ MYA 0.0002271 0.46808 4.0724
21 4WCX MET 0.04502 0.41299 4.0724
22 2JEV NHQ 0.001216 0.43838 4.5977
23 4NYT PC 0.00123 0.49235 4.60829
24 2YNE NHW 0.0007587 0.4579 5.42986
25 2YNE YNE 0.0007587 0.4579 5.42986
26 1IYK MYA 0.001644 0.40222 5.42986
27 1KUV CA5 0.0000275 0.4668 6.28019
28 4RHS SIA SIA GAL 0.02767 0.40765 6.55738
29 1PVC ILE SER GLU VAL 0.02918 0.40694 7.69231
30 5H86 BCO 0.0002029 0.42556 7.7381
31 1CM0 COA 0.01015 0.42247 7.7381
32 2Y2B AH0 0.0448 0.40249 9.09091
33 1WWZ ACO 0.0008071 0.43373 10.0629
34 1N71 COA 0.001557 0.44548 10.5556
35 2CNT COA 0.003154 0.42184 10.625
36 4PSW COA 0.0006832 0.47473 10.8597
37 1BOB ACO 0.0003681 0.40183 10.8597
38 2PZI AXX 0.02047 0.41106 12.2172
39 2Q4V ACO 0.0006445 0.40427 13.5294
40 1M4I COA 0.0003445 0.43708 16.5746
41 1M4I PAP 0.0003445 0.43708 16.5746
42 1M4I KAN 0.0003445 0.43708 16.5746
43 4AG9 COA 0.003067 0.45699 24.8485
44 5JPH COA 0.0000704 0.40951 38.1944
Pocket No.: 2; Query (leader) PDB : 5W8E; Ligand: ADE; Similar sites found: 40
This union binding pocket(no: 2) in the query (biounit: 5w8e.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QSR ACO 0.0001905 0.46802 None
2 1QSN COA 0.0008147 0.46085 None
3 1Q2D COA 0.001266 0.45628 None
4 2JDC CAO 0.0008898 0.4307 None
5 4U9W COA 0.006056 0.4058 1.93237
6 1CJW COT 0.0001248 0.43647 2.40964
7 1P0H ACO 0.003595 0.42267 2.71493
8 1P0H COA 0.003456 0.42267 2.71493
9 2ZFN ACO 0.005313 0.40816 3.16742
10 5FVJ ACO 0.001553 0.42412 3.61446
11 5K04 COA 0.009314 0.40349 3.61991
12 1I1D 16G 0.001048 0.41405 3.72671
13 1I1D COA 0.0003401 0.40649 3.72671
14 4H6U ACO 0.007796 0.40979 4
15 4UWJ 7L5 0.0002718 0.46791 4.0724
16 4UWJ MYA 0.0002718 0.46791 4.0724
17 2WDA L42 0.008375 0.44532 4.52489
18 2JEV NHQ 0.001132 0.44219 4.5977
19 2YNE YNE 0.0008949 0.45758 5.42986
20 2YNE NHW 0.0008949 0.45758 5.42986
21 1IYK MYA 0.001517 0.40765 5.42986
22 2YNC YNC 0.003296 0.40205 5.42986
23 1KUV CA5 0.00005544 0.46047 6.28019
24 5H86 BCO 0.0002456 0.42786 7.7381
25 1CM0 COA 0.009607 0.42247 7.7381
26 1IID NHM 0.00449 0.40138 9.50226
27 1WWZ ACO 0.0006985 0.43484 10.0629
28 4KVX ACO 0.0009992 0.40079 10.2564
29 1N71 COA 0.003869 0.42651 10.5556
30 2CNT COA 0.00303 0.42132 10.625
31 4PSW COA 0.0007657 0.47101 10.8597
32 1BOB ACO 0.000464 0.40202 10.8597
33 4MTI 2DX 0.04827 0.40361 11.3043
34 2PZI AXX 0.02217 0.4082 12.2172
35 2Q4V ACO 0.0006012 0.40851 13.5294
36 1M4I KAN 0.0003981 0.43759 16.5746
37 1M4I COA 0.0003981 0.43759 16.5746
38 1M4I PAP 0.0003981 0.43759 16.5746
39 4AG9 COA 0.01502 0.42056 24.8485
40 5JPH COA 0.0001094 0.40702 38.1944
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