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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 28 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 with APoc: 164
This union binding pocket(no: 1) in the query (biounit: 3p3g.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 4V1F BQ1 None
3 5H4S RAM 1.05634
4 4EKQ NPO 1.60428
5 5N26 73M 1.64835
6 2FN1 PYR 1.66667
7 6H8S FSZ 1.66667
8 1PVS 7HP 1.77305
9 6AP8 BNY 1.85874
10 4CP8 MLI 2
11 1F6D UDP 2
12 3X01 AMP 2
13 3TW1 AHN 2.1097
14 4DE3 DN8 2.28137
15 3AI3 SOL 2.28137
16 2WPX ACO 2.33333
17 6CB2 OLC 2.38908
18 2VWT PYR 2.62172
19 3TDC 0EU 2.66667
20 4KBA 1QM 2.66667
21 5XLA SIA 2.66667
22 4GYS MLI 2.66667
23 1D8C GLV 2.66667
24 2PYW SR1 2.66667
25 5U97 PIT 2.66667
26 6MDE MEV 2.66667
27 1RTF BEN 2.77778
28 1X0P FAD 2.7972
29 4WGF HX2 2.92683
30 6BXO SAH 3
31 2PSJ CEI 3
32 5ENZ UDP 3
33 2Q8G AZX 3
34 2D24 XYS XYS 3
35 2AZ3 CDP 3.04878
36 4V3I ASP LEU THR ARG PRO 3.11284
37 1SZO CAX 3.11284
38 4G86 BNT 3.16901
39 3F81 STT 3.27869
40 5LX9 OLB 3.33333
41 3RV5 DXC 3.37079
42 4XJ7 ADE 3.37079
43 3VY6 BGC BGC 3.5461
44 3GFZ FMN 3.66667
45 1NJJ GET 3.66667
46 5XQW 8EU 3.68664
47 2GWH PCI 3.69128
48 1XXR MAN 3.72671
49 3B6C SDN 3.84615
50 4M44 SIA GAL NAG GAL 3.84615
51 5F90 LMR 3.84615
52 5F90 GLA GAL 3.84615
53 5F90 GLA GAL BGC 5VQ 3.84615
54 3T03 3T0 3.87324
55 4TV1 36M 3.98406
56 4HDK 13X 4
57 6AC9 ANP 4
58 6FS0 E4W 4.12844
59 5XG5 A2G 4.13793
60 6D5V FVY 4.19162
61 6D5L FW7 4.19162
62 6D5J FV4 4.19162
63 6D5M FW4 4.19162
64 6D56 FVM 4.19162
65 6D5E FVG 4.19162
66 6D5G FVD 4.19162
67 6D55 FWA 4.19162
68 3OID TCL 4.26357
69 2BHW NEX 4.31034
70 5NE2 DGL 4.31655
71 2CYC TYR 4.33333
72 6E1Q CFA 4.33333
73 2HJ9 AI2 4.33333
74 2HZL PYR 4.33333
75 1JGS SAL 4.34783
76 5X3R 7Y3 4.39024
77 2YIV YIV 4.66667
78 1M2Z BOG 4.66926
79 4EHQ GBL 4.72973
80 1C3M MAN MAN 4.7619
81 2HYR BGC GLC 4.91803
82 2GUD BMA 4.91803
83 2GUD MAN 4.91803
84 2NU5 NAG 4.91803
85 2GUC MAN 4.91803
86 2NUO BGC 4.91803
87 2HYQ MAN MAN 4.91803
88 5K8P 6R8 5
89 1BW9 PPY 5
90 2F2U M77 5
91 1C1X HFA 5
92 1OYJ GSH 5
93 6BR8 6OU 5.15873
94 6BR8 PGV 5.15873
95 1I7Q PYR 5.18135
96 2HFN FMN 5.22876
97 3KP6 SAL 5.29801
98 2HHP FLC 5.33333
99 1Q11 TYE 5.33333
100 4NOS ITU 5.33333
101 5NNT DPV 5.40541
102 3FXU TSU 5.57377
103 6F90 MVL 5.66667
104 5VE5 GSH 5.66667
105 4TQK NAG 5.66667
106 3NZ1 3NY 5.74713
107 3KO0 TFP 5.94059
108 3AVR OGA 6
109 4E8C GAL 6
110 4NM5 ADP 6
111 3IX9 MTX 6.31579
112 2J5B TYE 6.33333
113 1Q8Y ADP 6.33333
114 4IA6 EIC 6.66667
115 3GD8 GOL 6.72646
116 2D5X L35 7.0922
117 3E7S AT2 7.33333
118 4HBM 0Y7 7.5
119 2BVE PH5 7.56302
120 2CYB TYR 7.66667
121 1TV5 N8E 7.66667
122 1MID LAP 7.69231
123 5I8F ML1 7.87879
124 4NSQ COA 7.89474
125 1MJT ITU 8
126 5YBL AKG 8
127 2BYC FMN 8.0292
128 4ISS TAR 8.33333
129 5EY0 GTP 8.39416
130 5LUB 3Y7 8.39695
131 1DTL BEP 8.69565
132 2PKA BEN 8.75
133 3JQQ A2P 9
134 3CM2 X23 9.23077
135 6FLZ MMA 9.72222
136 2Z48 A2G 10.3333
137 2Z48 NGA 10.3333
138 2Z49 AMG 10.3333
139 4RJD TFP 10.6061
140 1RV0 NDG 10.625
141 2GBB CIT 10.8974
142 6B74 BEN 11.1111
143 5MRH Q9Z 11.3333
144 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 11.5646
145 5X80 SAL 12.5
146 4YUS FMN 13
147 2Y69 CHD 13.75
148 4J24 EST 14.1667
149 2BCG GER 14.5631
150 1HBK COA 15.7303
151 5YRI GLC GLC 16.1972
152 5YRL GLC GLC 16.1972
153 5YRM BGC GLC 16.1972
154 5YRG BGC GLC 16.1972
155 5YRJ BGC GLC 16.1972
156 5YRF GLC GLC 16.1972
157 5N18 8HZ 18.3486
158 5ZCO CHD 18.6441
159 5Z84 CHD 18.6441
160 3TD3 GLY 18.6992
161 1IZC PYR 19
162 1JBU BEN 19.0476
163 3LQV ADE 23.0769
164 2WOR 2AN 25
Pocket No.: 2; Query (leader) PDB : 3P3G; Ligand: UKW; Similar sites found with APoc: 164
This union binding pocket(no: 2) in the query (biounit: 3p3g.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 4V1F BQ1 None
3 5H4S RAM 1.05634
4 4EKQ NPO 1.60428
5 5N26 73M 1.64835
6 2FN1 PYR 1.66667
7 6H8S FSZ 1.66667
8 1PVS 7HP 1.77305
9 6AP8 BNY 1.85874
10 4CP8 MLI 2
11 1F6D UDP 2
12 3X01 AMP 2
13 3TW1 AHN 2.1097
14 4DE3 DN8 2.28137
15 3AI3 SOL 2.28137
16 2WPX ACO 2.33333
17 6CB2 OLC 2.38908
18 2VWT PYR 2.62172
19 3TDC 0EU 2.66667
20 4KBA 1QM 2.66667
21 5XLA SIA 2.66667
22 4GYS MLI 2.66667
23 1D8C GLV 2.66667
24 2PYW SR1 2.66667
25 5U97 PIT 2.66667
26 6MDE MEV 2.66667
27 1RTF BEN 2.77778
28 1X0P FAD 2.7972
29 4WGF HX2 2.92683
30 6BXO SAH 3
31 2PSJ CEI 3
32 5ENZ UDP 3
33 2Q8G AZX 3
34 2D24 XYS XYS 3
35 2AZ3 CDP 3.04878
36 4V3I ASP LEU THR ARG PRO 3.11284
37 1SZO CAX 3.11284
38 4G86 BNT 3.16901
39 3F81 STT 3.27869
40 5LX9 OLB 3.33333
41 3RV5 DXC 3.37079
42 4XJ7 ADE 3.37079
43 3VY6 BGC BGC 3.5461
44 3GFZ FMN 3.66667
45 1NJJ GET 3.66667
46 5XQW 8EU 3.68664
47 2GWH PCI 3.69128
48 1XXR MAN 3.72671
49 3B6C SDN 3.84615
50 4M44 SIA GAL NAG GAL 3.84615
51 5F90 LMR 3.84615
52 5F90 GLA GAL 3.84615
53 5F90 GLA GAL BGC 5VQ 3.84615
54 3T03 3T0 3.87324
55 4TV1 36M 3.98406
56 4HDK 13X 4
57 6AC9 ANP 4
58 6FS0 E4W 4.12844
59 5XG5 A2G 4.13793
60 6D5V FVY 4.19162
61 6D5L FW7 4.19162
62 6D5J FV4 4.19162
63 6D5M FW4 4.19162
64 6D56 FVM 4.19162
65 6D5E FVG 4.19162
66 6D5G FVD 4.19162
67 6D55 FWA 4.19162
68 3OID TCL 4.26357
69 2BHW NEX 4.31034
70 5NE2 DGL 4.31655
71 2CYC TYR 4.33333
72 6E1Q CFA 4.33333
73 2HJ9 AI2 4.33333
74 2HZL PYR 4.33333
75 1JGS SAL 4.34783
76 5X3R 7Y3 4.39024
77 2YIV YIV 4.66667
78 1M2Z BOG 4.66926
79 4EHQ GBL 4.72973
80 1C3M MAN MAN 4.7619
81 2HYR BGC GLC 4.91803
82 2GUD BMA 4.91803
83 2GUD MAN 4.91803
84 2NU5 NAG 4.91803
85 2GUC MAN 4.91803
86 2NUO BGC 4.91803
87 2HYQ MAN MAN 4.91803
88 5K8P 6R8 5
89 1BW9 PPY 5
90 2F2U M77 5
91 1C1X HFA 5
92 1OYJ GSH 5
93 6BR8 6OU 5.15873
94 6BR8 PGV 5.15873
95 1I7Q PYR 5.18135
96 2HFN FMN 5.22876
97 3KP6 SAL 5.29801
98 2HHP FLC 5.33333
99 1Q11 TYE 5.33333
100 4NOS ITU 5.33333
101 5NNT DPV 5.40541
102 3FXU TSU 5.57377
103 6F90 MVL 5.66667
104 5VE5 GSH 5.66667
105 4TQK NAG 5.66667
106 3NZ1 3NY 5.74713
107 3KO0 TFP 5.94059
108 3AVR OGA 6
109 4E8C GAL 6
110 4NM5 ADP 6
111 3IX9 MTX 6.31579
112 2J5B TYE 6.33333
113 1Q8Y ADP 6.33333
114 4IA6 EIC 6.66667
115 3GD8 GOL 6.72646
116 2D5X L35 7.0922
117 3E7S AT2 7.33333
118 4HBM 0Y7 7.5
119 2BVE PH5 7.56302
120 2CYB TYR 7.66667
121 1TV5 N8E 7.66667
122 1MID LAP 7.69231
123 5I8F ML1 7.87879
124 4NSQ COA 7.89474
125 1MJT ITU 8
126 5YBL AKG 8
127 2BYC FMN 8.0292
128 4ISS TAR 8.33333
129 5EY0 GTP 8.39416
130 5LUB 3Y7 8.39695
131 1DTL BEP 8.69565
132 2PKA BEN 8.75
133 3JQQ A2P 9
134 3CM2 X23 9.23077
135 6FLZ MMA 9.72222
136 2Z48 A2G 10.3333
137 2Z48 NGA 10.3333
138 2Z49 AMG 10.3333
139 4RJD TFP 10.6061
140 1RV0 NDG 10.625
141 2GBB CIT 10.8974
142 6B74 BEN 11.1111
143 5MRH Q9Z 11.3333
144 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 11.5646
145 5X80 SAL 12.5
146 4YUS FMN 13
147 2Y69 CHD 13.75
148 4J24 EST 14.1667
149 2BCG GER 14.5631
150 1HBK COA 15.7303
151 5YRI GLC GLC 16.1972
152 5YRL GLC GLC 16.1972
153 5YRM BGC GLC 16.1972
154 5YRG BGC GLC 16.1972
155 5YRJ BGC GLC 16.1972
156 5YRF GLC GLC 16.1972
157 5N18 8HZ 18.3486
158 5ZCO CHD 18.6441
159 5Z84 CHD 18.6441
160 3TD3 GLY 18.6992
161 1IZC PYR 19
162 1JBU BEN 19.0476
163 3LQV ADE 23.0769
164 2WOR 2AN 25
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