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 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: SXZ; Similar ligands found: 138
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 XYA 0.494253 0.773333
20 ADN 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 SAI 0.480769 0.878378
27 G5A 0.480769 0.684783
28 EP4 0.478261 0.851351
29 A4D 0.477778 0.797297
30 LEU LMS 0.477477 0.725275
31 SAM 0.47619 0.894737
32 6RE 0.474227 0.7625
33 M2T 0.473118 0.853333
34 DSZ 0.472727 0.703297
35 VMS 0.472222 0.711111
36 54H 0.472222 0.711111
37 A5D 0.471154 0.789474
38 TSB 0.46789 0.681319
39 J7C 0.464646 0.772152
40 AMP 0.463918 0.707317
41 A 0.463918 0.707317
42 SMM 0.462963 0.884615
43 SSA 0.462963 0.684783
44 GSU 0.460177 0.722222
45 GJV 0.46 0.753086
46 52H 0.458716 0.703297
47 AAT 0.457944 0.820513
48 5AL 0.457944 0.765432
49 MHZ 0.456311 0.804878
50 CA0 0.456311 0.73494
51 NVA LMS 0.455357 0.706522
52 NEC 0.454545 0.75
53 53H 0.454545 0.703297
54 A3G 0.454545 0.802632
55 5CA 0.454545 0.684783
56 KB1 0.452174 0.833333
57 5AS 0.45098 0.666667
58 36A 0.45082 0.835443
59 GEK 0.45045 0.905405
60 8QN 0.45045 0.765432
61 ABM 0.45 0.710843
62 KH3 0.45 0.871795
63 IOT 0.448 0.75
64 KAA 0.447368 0.698925
65 SON 0.446602 0.768293
66 NSS 0.446429 0.684783
67 S4M 0.445545 0.8375
68 SRA 0.444444 0.694118
69 ME8 0.443478 0.819277
70 DAL AMP 0.441441 0.765432
71 MAO 0.441176 0.783133
72 AMP MG 0.44 0.690476
73 A6D 0.438596 0.705882
74 A3T 0.438095 0.8
75 A2D 0.435644 0.710843
76 A3N 0.435644 0.766234
77 ZAS 0.434343 0.746835
78 PRX 0.433962 0.756098
79 AMO 0.433628 0.768293
80 7MC 0.432 0.758621
81 NB8 0.431034 0.741176
82 AHX 0.429825 0.72093
83 ADX 0.428571 0.666667
84 M33 0.428571 0.722892
85 AU1 0.428571 0.694118
86 A12 0.427184 0.72619
87 BA3 0.427184 0.710843
88 AP2 0.427184 0.72619
89 VRT 0.425926 0.842105
90 AOC 0.425743 0.776316
91 2VA 0.424528 0.826667
92 SRP 0.423423 0.768293
93 B4P 0.423077 0.710843
94 AP5 0.423077 0.710843
95 ADP 0.423077 0.710843
96 5AD 0.422222 0.75
97 GAP 0.422018 0.73494
98 PAJ 0.421053 0.77381
99 4AD 0.421053 0.759036
100 APR 0.420561 0.731707
101 AR6 0.420561 0.731707
102 YLP 0.419355 0.77907
103 A3S 0.419048 0.813333
104 AN2 0.419048 0.702381
105 PTJ 0.418803 0.783133
106 RBY 0.416667 0.746988
107 ADV 0.416667 0.746988
108 XAH 0.416667 0.735632
109 SAP 0.416667 0.697674
110 YSA 0.416667 0.684783
111 AGS 0.416667 0.697674
112 ADP MG 0.415094 0.702381
113 SO8 0.412844 0.815789
114 WSA 0.412698 0.692308
115 BEF ADP 0.411215 0.686047
116 50T 0.411215 0.682353
117 ATP 0.411215 0.710843
118 ACP 0.411215 0.714286
119 ADP BEF 0.411215 0.686047
120 P5A 0.410256 0.709677
121 LAD 0.410256 0.77381
122 WAQ 0.410256 0.792683
123 ANP 0.409091 0.694118
124 TAT 0.409091 0.705882
125 APC 0.407407 0.72619
126 5FA 0.407407 0.710843
127 AQP 0.407407 0.710843
128 7MD 0.406504 0.755814
129 DLL 0.405172 0.743902
130 Y3J 0.404255 0.706667
131 ADP PO3 0.40367 0.728395
132 AD9 0.40367 0.694118
133 4YB 0.403226 0.706522
134 TAD 0.403226 0.732558
135 OAD 0.401709 0.756098
136 ARG AMP 0.4 0.727273
137 OOB 0.4 0.743902
138 ATP MG 0.4 0.702381
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: 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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