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Receptor
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.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:302;
Invalid;
none;
submit data
35.453 Cl [Cl-]
GOL A:303;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SXZ A:301;
Valid;
none;
submit data
468.527 C19 H28 N6 O6 S CC(C)...
ADE A:304;
Valid;
none;
submit data
135.127 C5 H5 N5 c1[nH...
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: SXZ; Similar ligands found: 144
No: Ligand ECFP6 Tc MDL keys Tc
1 SXZ 1 1
2 SAH 0.692308 0.916667
3 A7D 0.637363 0.851351
4 3DH 0.609195 0.824324
5 5X8 0.606383 0.888889
6 DSH 0.6 0.866667
7 DTA 0.574713 0.789474
8 S8M 0.563107 0.831169
9 MTA 0.550562 0.849315
10 TT8 0.543689 0.917808
11 SA8 0.514852 0.893333
12 5CD 0.511364 0.783784
13 S7M 0.504762 0.87013
14 K15 0.504587 0.883117
15 EEM 0.5 0.87013
16 62X 0.495413 0.909091
17 SFG 0.49505 0.875
18 RAB 0.494253 0.773333
19 ADN 0.494253 0.773333
20 XYA 0.494253 0.773333
21 0UM 0.486239 0.881579
22 LSS 0.486239 0.744444
23 5N5 0.483146 0.773333
24 TXA 0.482143 0.746988
25 A5A 0.481132 0.688889
26 G5A 0.480769 0.684783
27 SAI 0.480769 0.878378
28 EP4 0.478261 0.851351
29 A4D 0.477778 0.797297
30 SAM 0.47619 0.894737
31 6RE 0.474227 0.7625
32 M2T 0.473118 0.853333
33 DSZ 0.472727 0.703297
34 54H 0.472222 0.711111
35 VMS 0.472222 0.711111
36 A5D 0.471154 0.789474
37 NVA LMS 0.468468 0.717391
38 TSB 0.46789 0.681319
39 J7C 0.464646 0.772152
40 LEU LMS 0.464286 0.736264
41 LMS 0.463918 0.666667
42 AMP 0.463918 0.707317
43 A 0.463918 0.707317
44 9ZD 0.463636 0.75
45 9ZA 0.463636 0.75
46 SMM 0.462963 0.884615
47 SSA 0.462963 0.684783
48 GSU 0.460177 0.722222
49 GJV 0.46 0.753086
50 52H 0.458716 0.703297
51 5AL 0.457944 0.765432
52 AAT 0.457944 0.820513
53 MHZ 0.456311 0.804878
54 CA0 0.456311 0.73494
55 NEC 0.454545 0.75
56 5CA 0.454545 0.684783
57 A3G 0.454545 0.802632
58 53H 0.454545 0.703297
59 KB1 0.452174 0.833333
60 5AS 0.45098 0.666667
61 36A 0.45082 0.835443
62 8QN 0.45045 0.765432
63 GEK 0.45045 0.905405
64 ABM 0.45 0.710843
65 KH3 0.45 0.871795
66 IOT 0.448 0.75
67 KAA 0.447368 0.698925
68 SON 0.446602 0.768293
69 NSS 0.446429 0.684783
70 S4M 0.445545 0.8375
71 SRA 0.444444 0.694118
72 ME8 0.443478 0.819277
73 DAL AMP 0.441441 0.765432
74 MAO 0.441176 0.783133
75 A6D 0.438596 0.705882
76 A3T 0.438095 0.8
77 A2D 0.435644 0.710843
78 A3N 0.435644 0.766234
79 ZAS 0.434343 0.746835
80 PRX 0.433962 0.756098
81 AMO 0.433628 0.768293
82 8PZ 0.432203 0.684783
83 7MC 0.432 0.758621
84 F0P 0.432 0.893333
85 NB8 0.431034 0.741176
86 NVA 2AD 0.429907 0.831169
87 AHX 0.429825 0.72093
88 AU1 0.428571 0.694118
89 M33 0.428571 0.722892
90 ADX 0.428571 0.666667
91 8X1 0.428571 0.680851
92 A12 0.427184 0.72619
93 BA3 0.427184 0.710843
94 AP2 0.427184 0.72619
95 VRT 0.425926 0.842105
96 AOC 0.425743 0.776316
97 2VA 0.424528 0.826667
98 SRP 0.423423 0.768293
99 B4P 0.423077 0.710843
100 AP5 0.423077 0.710843
101 ADP 0.423077 0.710843
102 5AD 0.422222 0.75
103 GAP 0.422018 0.73494
104 PAJ 0.421053 0.77381
105 4AD 0.421053 0.759036
106 AR6 0.420561 0.731707
107 APR 0.420561 0.731707
108 YLP 0.419355 0.77907
109 AN2 0.419048 0.702381
110 A3S 0.419048 0.813333
111 AT4 0.419048 0.705882
112 PTJ 0.418803 0.783133
113 XAH 0.416667 0.735632
114 YSA 0.416667 0.684783
115 ADV 0.416667 0.746988
116 AGS 0.416667 0.697674
117 RBY 0.416667 0.746988
118 SAP 0.416667 0.697674
119 SO8 0.412844 0.815789
120 WSA 0.412698 0.692308
121 50T 0.411215 0.682353
122 ATP 0.411215 0.710843
123 HEJ 0.411215 0.710843
124 ACP 0.411215 0.714286
125 LAD 0.410256 0.77381
126 P5A 0.410256 0.709677
127 WAQ 0.410256 0.792683
128 T99 0.409091 0.705882
129 ANP 0.409091 0.694118
130 TAT 0.409091 0.705882
131 5FA 0.407407 0.710843
132 AQP 0.407407 0.710843
133 APC 0.407407 0.72619
134 9K8 0.40678 0.663158
135 7MD 0.406504 0.755814
136 ARG AMP 0.406504 0.727273
137 DLL 0.405172 0.743902
138 Y3J 0.404255 0.706667
139 AD9 0.40367 0.694118
140 ADP PO3 0.40367 0.728395
141 TAD 0.403226 0.732558
142 4YB 0.403226 0.706522
143 OAD 0.401709 0.756098
144 OOB 0.4 0.743902
Ligand no: 2; Ligand: ADE; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 ADE 1 1
2 PM6 0.5 0.742857
3 ES4 0.463415 0.685714
4 6AP 0.428571 0.9375
5 XQG 0.422222 0.648649
6 M02 0.411765 0.630435
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: 101
This union binding pocket(no: 1) in the query (biounit: 5w8e.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 1QSR ACO None
2 1PUA COA None
3 2IL4 COA None
4 1QSN COA None
5 1Q2D COA None
6 2JDC CAO None
7 1Q2C COA None
8 1OJZ NAD None
9 4RI1 ACO None
10 4KBA 1QM 1.80995
11 4U9W COA 1.93237
12 1BO4 COA 2.38095
13 4GAH 0ET 2.39234
14 1CJW COT 2.40964
15 5HGZ ACO 2.71493
16 1P0H COA 2.71493
17 1P0H ACO 2.71493
18 1GHE ACO 2.82486
19 5HH0 COA 3
20 2ZFN ACO 3.16742
21 6BA2 7KM 3.16742
22 1TIQ COA 3.33333
23 5FVJ ACO 3.61446
24 2WSA MYA 3.61991
25 2WSA 646 3.61991
26 2WPX ACO 3.61991
27 4O8A 2OP 3.61991
28 5K04 COA 3.61991
29 1I1D COA 3.72671
30 1I1D 16G 3.72671
31 1KZL CRM 3.84615
32 4QPL V3L 3.87097
33 4H6U ACO 4
34 5YGE ACO 4.02299
35 4UWJ 7L5 4.0724
36 4UWJ MYA 4.0724
37 4WCX MET 4.0724
38 5XJD 87L 4.09091
39 1U9L ASN ARG PRO ILE LEU SER LEU 4.28571
40 1S7N COA 4.3956
41 2WPW ACO 4.52489
42 2JEV NHQ 4.5977
43 1QSM ACO 4.60526
44 4NYT PC 4.60829
45 3TE4 ACO 4.65116
46 3SXN COA 4.97738
47 2YNE NHW 5.42986
48 2YNE YNE 5.42986
49 2IZ1 ATR 5.42986
50 1IYK MYA 5.42986
51 4L80 1VU 5.42986
52 4UA3 COA 5.6701
53 3WR7 COA 5.88235
54 5GK9 ACO 6
55 5XXS COA 6.06061
56 1KUV CA5 6.28019
57 1VPE 3PG 6.33484
58 4WQQ MAN 6.38298
59 4RHS SIA SIA GAL 6.55738
60 5LY1 PPI 6.78733
61 5KF9 COA 7.23982
62 5KF9 NAG 7.23982
63 3TO7 COA 7.23982
64 4C2X NHW 7.23982
65 5KF9 ACO 7.23982
66 6EYT UDP 7.23982
67 5VNB ALA THR ALY ALA ALA ARG ALY SER ALA PRO 7.43243
68 1PVC ILE SER GLU VAL 7.69231
69 5Y79 3PG 7.69231
70 5H86 BCO 7.7381
71 1CM0 COA 7.7381
72 4R57 ACO 7.95455
73 3JQ9 AX1 8.1448
74 4N14 WR7 8.1448
75 2Y2B AH0 9.09091
76 2ZPA ACO 9.50226
77 5TVJ COA 9.50226
78 5TVJ 7LF 9.50226
79 1WWZ ACO 10.0629
80 4KVX ACO 10.2564
81 1N71 COA 10.5556
82 2CNT COA 10.625
83 4PSW COA 10.8597
84 1BOB ACO 10.8597
85 5LXB 7A9 11.157
86 4NSQ COA 11.3122
87 3D2M COA 12.2172
88 2PZI AXX 12.2172
89 2Q4V ACO 13.5294
90 1M4I KAN 16.5746
91 1M4I COA 16.5746
92 1M4I PAP 16.5746
93 2VBQ BSJ 16.9697
94 5MU6 MYA 17.1946
95 5MU6 KFK 17.1946
96 1YAA MAE 17.6471
97 2B4D COA 19.883
98 2B4B COA 19.883
99 6G96 ACO 20.4545
100 4AG9 COA 24.8485
101 5JPH COA 38.1944
Pocket No.: 2; Query (leader) PDB : 5W8E; Ligand: ADE; Similar sites found with APoc: 91
This union binding pocket(no: 2) in the query (biounit: 5w8e.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 1PUA COA None
2 1QSR ACO None
3 2IL4 COA None
4 1QSN COA None
5 1Q2D COA None
6 1Q2C COA None
7 2JDC CAO None
8 4RI1 ACO None
9 4U9W COA 1.93237
10 1BO4 COA 2.38095
11 4GAH 0ET 2.39234
12 1CJW COT 2.40964
13 1P0H ACO 2.71493
14 1P0H COA 2.71493
15 5HGZ ACO 2.71493
16 1GHE ACO 2.82486
17 5HH0 COA 3
18 2ZFN ACO 3.16742
19 6BA2 7KM 3.16742
20 1TIQ COA 3.33333
21 5FVJ ACO 3.61446
22 2WSA 646 3.61991
23 2WSA MYA 3.61991
24 2WPX ACO 3.61991
25 4O8A 2OP 3.61991
26 5K04 COA 3.61991
27 1I1D COA 3.72671
28 1I1D 16G 3.72671
29 4QPL V3L 3.87097
30 4H6U ACO 4
31 5YGE ACO 4.02299
32 4UWJ 7L5 4.0724
33 4UWJ MYA 4.0724
34 1U9L ASN ARG PRO ILE LEU SER LEU 4.28571
35 1S7N COA 4.3956
36 2WDA L42 4.52489
37 2WPW ACO 4.52489
38 2JEV NHQ 4.5977
39 1QSM ACO 4.60526
40 3TE4 ACO 4.65116
41 1WK8 VMS 5.15464
42 2YNE NHW 5.42986
43 2YNE YNE 5.42986
44 1IYK MYA 5.42986
45 2YNC YNC 5.42986
46 4UA3 COA 5.6701
47 3WR7 COA 5.88235
48 5GK9 ACO 6
49 5XXS COA 6.06061
50 1KUV CA5 6.28019
51 5KF9 NAG 7.23982
52 5KF9 COA 7.23982
53 3TO7 COA 7.23982
54 4C2X NHW 7.23982
55 5KF9 ACO 7.23982
56 6EYT UDP 7.23982
57 4ZW9 BGC 7.69231
58 4ZW9 GLC 7.69231
59 5H86 BCO 7.7381
60 1CM0 COA 7.7381
61 4R57 ACO 7.95455
62 3JQ9 AX1 8.1448
63 4N14 WR7 8.1448
64 2ZPA ACO 9.50226
65 5TVJ COA 9.50226
66 5TVJ 7LF 9.50226
67 1IID NHM 9.50226
68 1WWZ ACO 10.0629
69 4KVX ACO 10.2564
70 1N71 COA 10.5556
71 2CNT COA 10.625
72 4PSW COA 10.8597
73 1BOB ACO 10.8597
74 5LXB 7A9 11.157
75 4MTI 2DX 11.3043
76 4NSQ COA 11.3122
77 3D2M COA 12.2172
78 2PZI AXX 12.2172
79 2Q4V ACO 13.5294
80 1M4I PAP 16.5746
81 1M4I COA 16.5746
82 1M4I KAN 16.5746
83 2VBQ BSJ 16.9697
84 5MU6 MYA 17.1946
85 5MU6 KFK 17.1946
86 1YAA MAE 17.6471
87 2B4D COA 19.883
88 2B4B COA 19.883
89 6G96 ACO 20.4545
90 4AG9 COA 24.8485
91 5JPH COA 38.1944
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