Receptor
PDB id Resolution Class Description Source Keywords
3P3G 1.65 Å EC: 3.5.1.33 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/LPC-009 COMPL ESCHERICHIA COLI LIPID A BIOSYNTHESIS LIPID A SYNTHESIS LPXC BAAB SANDWICHHYDROLASE DEACETYLATION ANTIBIOTIC ACYL UDP-GLCNAC HYDRLPC-009
Ref.: SPECIES-SPECIFIC AND INHIBITOR-DEPENDENT CONFORMATI LPXC: IMPLICATIONS FOR ANTIBIOTIC DESIGN. CHEM.BIOL. V. 18 38 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3P3 A:401;
Valid;
none;
Ki = 0.18 nM
362.379 C21 H18 N2 O4 C[C@H...
DMS A:701;
Invalid;
none;
submit data
78.133 C2 H6 O S CS(=O...
SO4 A:501;
A:502;
A:504;
A:505;
A:506;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
UKW A:801;
Valid;
none;
submit data
260.245 C13 H12 N2 O4 C[C@H...
ZN A:301;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3P3G 1.65 Å EC: 3.5.1.33 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/LPC-009 COMPL ESCHERICHIA COLI LIPID A BIOSYNTHESIS LIPID A SYNTHESIS LPXC BAAB SANDWICHHYDROLASE DEACETYLATION ANTIBIOTIC ACYL UDP-GLCNAC HYDRLPC-009
Ref.: SPECIES-SPECIFIC AND INHIBITOR-DEPENDENT CONFORMATI LPXC: IMPLICATIONS FOR ANTIBIOTIC DESIGN. CHEM.BIOL. V. 18 38 2011
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
2 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
3 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
4 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
5 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
6 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
7 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 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 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
15 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
16 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
17 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
18 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
19 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
20 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
21 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
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: 3P3; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 3P3 1 1
2 ZH2 0.754098 0.913043
3 5EP 0.557143 0.75
4 L53 0.528571 0.791667
5 ZH4 0.513158 0.791667
6 C90 0.5 0.677419
7 1WM 0.487179 0.854167
8 5EM 0.465753 0.764706
9 5EN 0.435897 0.807692
10 P76 0.421687 0.666667
11 1WN 0.411765 0.84
12 UKW 0.405797 0.818182
13 1JS 0.4 0.696429
14 1WL 0.4 0.644068
Ligand no: 2; Ligand: UKW; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 UKW 1 1
2 L53 0.627119 0.863636
3 ZH4 0.552239 0.863636
4 ZH2 0.411765 0.75
5 3P3 0.405797 0.818182
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3P3G; Ligand: 3P3; Similar sites found: 66
This union binding pocket(no: 1) in the query (biounit: 3p3g.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FN1 PYR 0.009223 0.44368 1.66667
2 1PVS 7HP 0.005163 0.41528 1.77305
3 4CP8 MLI 0.01313 0.42913 2
4 1F6D UDP 0.009349 0.42599 2
5 3X01 AMP 0.03373 0.40711 2
6 3TW1 AHN 0.04283 0.40167 2.1097
7 3AI3 SOL 0.03008 0.40816 2.28137
8 2WPX ACO 0.006602 0.41424 2.33333
9 3TDC 0EU 0.00001242 0.65383 2.66667
10 4KBA 1QM 0.007211 0.4362 2.66667
11 5XLA SIA 0.01229 0.43085 2.66667
12 4GYS MLI 0.02101 0.41646 2.66667
13 1D8C GLV 0.03018 0.41408 2.66667
14 2PYW SR1 0.02702 0.41238 2.66667
15 1X0P FAD 0.01285 0.41133 2.7972
16 4WGF HX2 0.006577 0.44043 2.92683
17 2PSJ CEI 0.0146 0.42486 3
18 2D24 XYS XYS 0.03794 0.40739 3
19 4V3I ASP LEU THR ARG PRO 0.0263 0.4145 3.11284
20 1SZO CAX 0.04489 0.40027 3.11284
21 3VY6 BGC BGC 0.005722 0.46504 3.5461
22 1NJJ GET 0.03325 0.40692 3.66667
23 3B6C SDN 0.01588 0.42292 3.84615
24 5F90 LMR 0.02282 0.41334 3.84615
25 5F90 GLA GAL 0.02906 0.41125 3.84615
26 5F90 GLA GAL BGC 5VQ 0.03478 0.40599 3.84615
27 4HDK 13X 0.02279 0.41459 4
28 5NE2 DGL 0.03554 0.40418 4.31655
29 2CYC TYR 0.002093 0.47085 4.33333
30 2HYR BGC GLC 0.01534 0.43818 4.91803
31 2GUD BMA 0.01742 0.43685 4.91803
32 2GUD MAN 0.01844 0.43338 4.91803
33 2NU5 NAG 0.01856 0.4332 4.91803
34 2GUC MAN 0.01879 0.43274 4.91803
35 2NUO BGC 0.02498 0.42887 4.91803
36 1C1X HFA 0.0177 0.40823 5
37 1I7Q PYR 0.01663 0.42405 5.18135
38 2HHP FLC 0.01487 0.44245 5.33333
39 4NOS ITU 0.02561 0.40777 5.33333
40 5VE5 GSH 0.01933 0.41532 5.66667
41 3NZ1 3NY 0.02673 0.41659 5.74713
42 3AVR OGA 0.01626 0.42351 6
43 4E8C GAL 0.01886 0.41465 6
44 3IX9 MTX 0.01585 0.41058 6.31579
45 2J5B TYE 0.03186 0.40557 6.33333
46 1Q8Y ADP 0.01003 0.40293 6.33333
47 3E7S AT2 0.004328 0.45683 7.33333
48 4HBM 0Y7 0.01234 0.40861 7.5
49 2BVE PH5 0.0234 0.4106 7.56302
50 2CYB TYR 0.002744 0.4636 7.66667
51 1TV5 N8E 0.02906 0.42209 7.66667
52 4NSQ COA 0.01083 0.40783 7.89474
53 1KTG AMP 0.03054 0.40373 7.97101
54 1MJT ITU 0.00235 0.45581 8
55 2BYC FMN 0.01974 0.40588 8.0292
56 4ISS TAR 0.0246 0.4146 8.33333
57 5LUB 3Y7 0.0277 0.41062 8.39695
58 1Y7P RIP 0.002195 0.40151 8.52018
59 2PKA BEN 0.02067 0.41906 8.75
60 3CM2 X23 0.02709 0.41168 9.23077
61 5AAN XOC 0.01974 0.41997 10.6952
62 2GBB CIT 0.02585 0.41167 10.8974
63 5MRH Q9Z 0.01488 0.41998 11.3333
64 2BCG GER 0.004665 0.44593 14.5631
65 5N18 8HZ 0.03168 0.40862 18.3486
66 3LQV ADE 0.02934 0.41958 23.0769
Pocket No.: 2; Query (leader) PDB : 3P3G; Ligand: UKW; Similar sites found: 66
This union binding pocket(no: 2) in the query (biounit: 3p3g.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FN1 PYR 0.009223 0.44368 1.66667
2 1PVS 7HP 0.005163 0.41528 1.77305
3 4CP8 MLI 0.01313 0.42913 2
4 1F6D UDP 0.009349 0.42599 2
5 3X01 AMP 0.03373 0.40711 2
6 3TW1 AHN 0.04283 0.40167 2.1097
7 3AI3 SOL 0.03008 0.40816 2.28137
8 2WPX ACO 0.006602 0.41424 2.33333
9 3TDC 0EU 0.00001242 0.65383 2.66667
10 4KBA 1QM 0.007211 0.4362 2.66667
11 5XLA SIA 0.01229 0.43085 2.66667
12 4GYS MLI 0.02101 0.41646 2.66667
13 1D8C GLV 0.03018 0.41408 2.66667
14 2PYW SR1 0.02702 0.41238 2.66667
15 1X0P FAD 0.01285 0.41133 2.7972
16 4WGF HX2 0.006577 0.44043 2.92683
17 2PSJ CEI 0.0146 0.42486 3
18 2D24 XYS XYS 0.03794 0.40739 3
19 4V3I ASP LEU THR ARG PRO 0.0263 0.4145 3.11284
20 1SZO CAX 0.04489 0.40027 3.11284
21 3VY6 BGC BGC 0.005722 0.46504 3.5461
22 1NJJ GET 0.03325 0.40692 3.66667
23 3B6C SDN 0.01588 0.42292 3.84615
24 5F90 LMR 0.02282 0.41334 3.84615
25 5F90 GLA GAL 0.02906 0.41125 3.84615
26 5F90 GLA GAL BGC 5VQ 0.03478 0.40599 3.84615
27 4HDK 13X 0.02279 0.41459 4
28 5NE2 DGL 0.03554 0.40418 4.31655
29 2CYC TYR 0.002093 0.47085 4.33333
30 2HYR BGC GLC 0.01534 0.43818 4.91803
31 2GUD BMA 0.01742 0.43685 4.91803
32 2GUD MAN 0.01844 0.43338 4.91803
33 2NU5 NAG 0.01856 0.4332 4.91803
34 2GUC MAN 0.01879 0.43274 4.91803
35 2NUO BGC 0.02498 0.42887 4.91803
36 1C1X HFA 0.0177 0.40823 5
37 1I7Q PYR 0.01663 0.42405 5.18135
38 2HHP FLC 0.01487 0.44245 5.33333
39 4NOS ITU 0.02561 0.40777 5.33333
40 5VE5 GSH 0.01933 0.41532 5.66667
41 3NZ1 3NY 0.02673 0.41659 5.74713
42 3AVR OGA 0.01626 0.42351 6
43 4E8C GAL 0.01886 0.41465 6
44 3IX9 MTX 0.01585 0.41058 6.31579
45 2J5B TYE 0.03186 0.40557 6.33333
46 1Q8Y ADP 0.01003 0.40293 6.33333
47 3E7S AT2 0.004328 0.45683 7.33333
48 4HBM 0Y7 0.01234 0.40861 7.5
49 2BVE PH5 0.0234 0.4106 7.56302
50 2CYB TYR 0.002744 0.4636 7.66667
51 1TV5 N8E 0.02906 0.42209 7.66667
52 4NSQ COA 0.01083 0.40783 7.89474
53 1KTG AMP 0.03054 0.40373 7.97101
54 1MJT ITU 0.00235 0.45581 8
55 2BYC FMN 0.01974 0.40588 8.0292
56 4ISS TAR 0.0246 0.4146 8.33333
57 5LUB 3Y7 0.0277 0.41062 8.39695
58 1Y7P RIP 0.002195 0.40151 8.52018
59 2PKA BEN 0.02067 0.41906 8.75
60 3CM2 X23 0.02709 0.41168 9.23077
61 5AAN XOC 0.01974 0.41997 10.6952
62 2GBB CIT 0.02585 0.41167 10.8974
63 5MRH Q9Z 0.01488 0.41998 11.3333
64 2BCG GER 0.004665 0.44593 14.5631
65 5N18 8HZ 0.03168 0.40862 18.3486
66 3LQV ADE 0.02934 0.41958 23.0769
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