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 27 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 25 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: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Ligand no: 2; Ligand: UDP; Similar ligands found: 116
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 UPU 0.72973 0.940298
6 2KH 0.722222 0.970149
7 44P 0.720588 0.955882
8 URM 0.717949 0.927536
9 GUD 0.717949 0.941176
10 GDU 0.717949 0.941176
11 UFM 0.717949 0.941176
12 UPG 0.717949 0.941176
13 660 0.717949 0.927536
14 UDP UDP 0.714286 0.939394
15 UDH 0.705128 0.864865
16 UPP 0.705128 0.941176
17 UPF 0.691358 0.888889
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UDX 0.670732 0.941176
21 UAD 0.670732 0.941176
22 3UC 0.658824 0.888889
23 USQ 0.654762 0.820513
24 UGB 0.654762 0.955224
25 UGA 0.654762 0.955224
26 G3N 0.647059 0.914286
27 UDM 0.636364 0.914286
28 URI 0.625 0.863636
29 U 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 UDP GAL 0.611765 0.913043
33 Y6W 0.607143 0.888889
34 CDP 0.605263 0.942029
35 UD7 0.591398 0.927536
36 HP7 0.591398 0.941176
37 MJZ 0.585106 0.914286
38 IUG 0.583333 0.810127
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 UD4 0.578947 0.914286
42 CJB 0.573529 0.820895
43 UDZ 0.571429 0.853333
44 DUD 0.571429 0.913043
45 UP5 0.571429 0.853333
46 U U 0.563218 0.955224
47 EPZ 0.56 0.914286
48 5GW 0.559524 0.942029
49 EPU 0.554455 0.901408
50 EEB 0.554455 0.901408
51 UA3 0.547945 0.939394
52 U3P 0.547945 0.939394
53 CH 0.546667 0.913043
54 4TC 0.544554 0.831169
55 CTP 0.54321 0.942029
56 CSV 0.531915 0.851351
57 CSQ 0.531915 0.851351
58 DUT 0.52439 0.913043
59 4GW 0.516484 0.915493
60 UMA 0.513761 0.914286
61 U4S 0.513158 0.753425
62 U2P 0.506667 0.954545
63 U2S 0.5 0.767123
64 U3S 0.5 0.753425
65 PUP 0.48913 0.913043
66 U22 0.486957 0.790123
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 DKX 0.486486 0.746479
70 U1S 0.482759 0.75
71 A U 0.481132 0.805195
72 2QR 0.478632 0.822785
73 5FU 0.474359 0.914286
74 8OD 0.47191 0.851351
75 C5G 0.468085 0.888889
76 7XL 0.465909 0.888889
77 U U U U 0.461538 0.940298
78 UMF 0.461538 0.857143
79 G8D 0.460674 0.855263
80 UTP U U U 0.456522 0.895522
81 2TU 0.452055 0.774648
82 4RA 0.451613 0.855263
83 C2G 0.450549 0.901408
84 DU 0.45 0.898551
85 CAR 0.45 0.927536
86 C 0.45 0.927536
87 C5P 0.45 0.927536
88 UMP 0.45 0.898551
89 UAG 0.448 0.864865
90 CDC 0.446809 0.777778
91 UD0 0.444444 0.844156
92 5BU 0.444444 0.914286
93 N3E 0.440476 0.733333
94 UC5 0.440476 0.9
95 UUA 0.438356 0.772727
96 DUP 0.431818 0.887324
97 2GW 0.431373 0.901408
98 M7G 0.430108 0.780488
99 CNU 0.428571 0.927536
100 CDM 0.427083 0.842105
101 H6Y 0.425532 0.851351
102 16B 0.421687 0.888889
103 S5P 0.419753 0.915493
104 8GT 0.419355 0.855263
105 CXY 0.418367 0.888889
106 UPA 0.418182 0.842105
107 CDP MG 0.413793 0.849315
108 U2G 0.410714 0.822785
109 U A A U 0.409836 0.842105
110 UML 0.408759 0.810127
111 UP6 0.407407 0.871429
112 M7M 0.40625 0.771084
113 PMP UD1 0.404762 0.794872
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found: 12
This union binding pocket(no: 1) in the query (biounit: 2o3z.bio3) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.01165 0.44369 None
2 5T96 79J 0.04394 0.40193 1.47601
3 5U83 ZN8 0.04594 0.40286 1.88679
4 5KAX RHQ 0.03532 0.40908 3.01205
5 4Z2S NAG 0.04777 0.40214 3.52113
6 4Z2S NDG 0.04777 0.40214 3.52113
7 3R75 PYR 0.03616 0.40308 4.42804
8 4ZM4 PLP 0.01828 0.40883 4.79705
9 5HWK BEZ 0.01746 0.42452 5.41667
10 4RJD TFP 0.04324 0.40907 9.09091
11 3ZJX BOG 0.02636 0.41409 9.22509
12 5EXA 5SO 0.02123 0.41682 11.7391
Pocket No.: 2; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found: 16
This union binding pocket(no: 2) in the query (biounit: 2o3z.bio1) has 68 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VY6 BGC BGC 0.01391 0.45536 None
2 4UAI 3GG 0.01142 0.45071 None
3 1FLJ GSH 0.04278 0.41705 1.53846
4 1PS6 4TP 0.01235 0.45287 1.84502
5 2FN1 PYR 0.03012 0.42884 2.58303
6 4BLW AMP 0.04976 0.42098 2.95203
7 4L1F COS 0.02648 0.40799 2.95203
8 2CYB TYR 0.01538 0.45663 4.42804
9 1MJT ITU 0.008204 0.4587 5.16605
10 5F1H 5U6 0.02328 0.44151 5.69106
11 3X01 AMP 0.01312 0.46084 7.38007
12 2CYC TYR 0.03235 0.43822 7.38007
13 3CF6 SP1 0.04819 0.41062 9.5941
14 1WZ1 DNS 0.03606 0.43613 11.5044
15 4S15 4D8 0.03409 0.4076 12.8906
16 4ZYB 4SQ 0.04738 0.42763 24.6269
Pocket No.: 3; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found: 16
This union binding pocket(no: 4) in the query (biounit: 2o3z.bio2) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1MAI I3P 0.02579 0.41025 None
2 1SYN UMP 0.02017 0.41247 1.88679
3 4ISK UMP 0.02246 0.4138 1.89394
4 2CUN 3PG 0.04345 0.41506 2.21402
5 4XWM CBI 0.03021 0.41579 2.58303
6 4WCX ALA 0.01626 0.4121 2.91667
7 4FBL SPD 0.03462 0.40774 2.95203
8 2VHL GLP 0.03388 0.40454 2.95203
9 2OFE NAG 0.04602 0.4051 3.52113
10 4URN NOV 0.03693 0.41014 3.55556
11 1J3I UMP 0.0205 0.41585 6.40244
12 2ICK DMA 0.02876 0.40467 6.43777
13 2VDF OCT 0.02188 0.43883 6.71937
14 5NBW 8SK 0.01462 0.4195 8.41121
15 1GAW FAD 0.02781 0.40204 11.4391
16 1Y7P RIP 0.006337 0.42796 14.3498
Pocket No.: 5; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2O3Z; Ligand: AI7; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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