Receptor
PDB id Resolution Class Description Source Keywords
2J65 2.2 Å EC: 3.5.1.- STRUCTURE OF LPXC FROM AQUIFEX AEOLICUS IN COMPLEX WITH UDP AQUIFEX AEOLICUS HYDROLASE LIPID SYNTHESIS LIPID A BIOSYNTHESIS
Ref.: THE NUCLEOTIDE-BINDING SITE OF AQUIFEX AEOLICUS LPX ACTA CRYSTALLOGR.,SECT.F V. 62 1082 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:305;
B:304;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
MYR A:401;
B:401;
B:403;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
228.371 C14 H28 O2 CCCCC...
UDP A:402;
B:402;
 Valid;
Valid;
 none;
none;
 submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
ZN A:301;
A:302;
A:303;
A:304;
B:301;
B:302;
B:303;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2O3Z 2.25 Å EC: 3.5.1.- X-RAY CRYSTAL STRUCTURE OF LPXC COMPLEXED WITH 3-HEPTYLOXYBE AQUIFEX AEOLICUS LIPID A BIOSYNTHESIS LIPID SYNTHESIS LPXC 3-HEPTYLOXYBENZHYDROLASE
Ref.: AMPHIPATHIC BENZOIC ACID DERIVATIVES: SYNTHESIS AND IN THE HYDROPHOBIC TUNNEL OF THE ZINC DEACETYLASE L BIOORG.MED.CHEM. V. 15 2617 2007
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
2 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
3 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
4 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
5 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
6 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
7 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
8 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
9 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
10 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
2 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
3 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
4 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
5 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
6 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
7 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
8 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
9 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
10 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
14 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
15 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
16 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
17 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
18 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
19 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
20 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
21 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
22 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
23 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
24 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
25 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
26 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
27 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
28 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
29 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
30 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
31 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MYR; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 EW8 1 1
3 TDA 1 1
4 F15 1 1
5 PLM 1 1
6 STE 1 1
7 X90 1 1
8 DAO 1 1
9 KNA 1 1
10 DCR 1 1
11 F23 1 1
12 11A 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 OLA 0.71875 0.954545
21 NER 0.71875 0.954545
22 VCA 0.666667 0.954545
23 PAM 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EIC 0.538462 0.913043
35 EOD 0.538462 0.7
36 D0G 0.5 0.954545
37 BMJ 0.5 0.954545
38 BNV 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 HXD 0.459459 0.807692
43 56S 0.459459 0.653846
44 ODT 0.452381 0.782609
45 3X1 0.444444 0.818182
46 LNL 0.44186 0.826087
47 9J6 0.441176 0.666667
48 OOA 0.441176 0.76
49 CUY 0.435897 0.68
50 6UL 0.435897 0.68
51 CNS 0.435897 0.68
52 5UF 0.432432 0.807692
53 243 0.428571 0.807692
54 1QW 0.418605 0.606061
55 GYM 0.418605 0.606061
56 O8N 0.413793 0.75
57 1DO 0.413793 0.75
58 PL3 0.413793 0.75
59 OC9 0.413793 0.75
60 DE1 0.413793 0.75
61 F09 0.413793 0.75
62 T25 0.403846 0.677419
Ligand no: 2; Ligand: UDP; Similar ligands found: 117
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2O3Z; Ligand: AI7; 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: 2o3z.bio3) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2O3Z; Ligand: AI7; 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: 2o3z.bio1) has 68 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2o3z.bio1) has 68 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2o3z.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2o3z.bio2) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2o3z.bio4) has 35 residues
No: Leader PDB Ligand Sequence Similarity
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