Receptor
PDB id Resolution Class Description Source Keywords
3ED0 2.3 Å EC: 4.2.1.- CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX WITHE MODIN HELICOBACTER PYLORI FABZ COMPLEX EMODIN CYTOPLASM LIPID A BIOSYNTHESIS LIPIDSYNTHESIS LYASE
Ref.: EMODIN TARGETS THE BETA-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE FROM HELICOBACTER PYLORI: ENZYMATIC INHIBITION ASSAY WITH CRYSTAL STRUCTURAL AND THERMODYNAMIC CHARACTERIZATION BMC MICROBIOL. V. 9 91 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BEN A:160;
A:161;
B:160;
B:161;
D:160;
E:160;
E:161;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
120.152 C7 H8 N2 [H]/N...
CL A:162;
B:162;
C:160;
D:161;
E:162;
F:160;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
EMO A:163;
C:161;
Valid;
Valid;
none;
none;
Kd = 0.45 uM
270.237 C15 H10 O5 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3D04 2.4 Å EC: 4.2.1.- CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX W ITH SAKURANETIN HELICOBACTER PYLORI FABZ COMPLEX SAKURANETIN LYASE
Ref.: THREE FLAVONOIDS TARGETING THE BETA-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE FROM HELICOBACTER PYLORI: CRYSTAL STRUCTURE CHARACTERIZATION WITH ENZYMATIC INHIBITION ASSAY PROTEIN SCI. V. 17 1971 2008
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3CF8 Ki = 12.7 uM QUE C15 H10 O7 c1cc(c(cc1....
2 3DOZ ic50 = 1.98 uM 3BE C14 H9 Br3 N2 O3 c1cc(cc(c1....
3 3ED0 Kd = 0.45 uM EMO C15 H10 O5 Cc1cc2c(c(....
4 3B7J Ki = 6.8 uM JUG C10 H6 O3 c1cc2c(c(c....
5 3DP3 ic50 = 1.52 uM 4BB C18 H18 Br2 N2 O3 CC(C)(C)c1....
6 3DP2 ic50 = 1.5 uM 4BE C14 H9 Br3 N2 O3 c1cc(ccc1C....
7 3DP1 ic50 = 9.92 uM 2RB C15 H12 Br2 N2 O4 COc1ccc(cc....
8 3D04 Ki = 0.9 uM SAK C16 H14 O5 COc1cc(c2c....
9 3DP0 ic50 = 1.42 uM 2BC C18 H12 Br2 N2 O3 c1ccc2cc(c....
10 3DOY ic50 = 1.52 uM 2BE C14 H9 Br2 Cl N2 O3 c1cc(ccc1C....
11 2GLP ic50 = 39.8 uM BDE C13 H9 Br2 N3 O3 c1cc(cnc1)....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3CF8 Ki = 12.7 uM QUE C15 H10 O7 c1cc(c(cc1....
2 3DOZ ic50 = 1.98 uM 3BE C14 H9 Br3 N2 O3 c1cc(cc(c1....
3 3ED0 Kd = 0.45 uM EMO C15 H10 O5 Cc1cc2c(c(....
4 3B7J Ki = 6.8 uM JUG C10 H6 O3 c1cc2c(c(c....
5 3DP3 ic50 = 1.52 uM 4BB C18 H18 Br2 N2 O3 CC(C)(C)c1....
6 3DP2 ic50 = 1.5 uM 4BE C14 H9 Br3 N2 O3 c1cc(ccc1C....
7 3DP1 ic50 = 9.92 uM 2RB C15 H12 Br2 N2 O4 COc1ccc(cc....
8 3D04 Ki = 0.9 uM SAK C16 H14 O5 COc1cc(c2c....
9 3DP0 ic50 = 1.42 uM 2BC C18 H12 Br2 N2 O3 c1ccc2cc(c....
10 3DOY ic50 = 1.52 uM 2BE C14 H9 Br2 Cl N2 O3 c1cc(ccc1C....
11 2GLP ic50 = 39.8 uM BDE C13 H9 Br2 N3 O3 c1cc(cnc1)....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3CF8 Ki = 12.7 uM QUE C15 H10 O7 c1cc(c(cc1....
2 3DOZ ic50 = 1.98 uM 3BE C14 H9 Br3 N2 O3 c1cc(cc(c1....
3 3ED0 Kd = 0.45 uM EMO C15 H10 O5 Cc1cc2c(c(....
4 3B7J Ki = 6.8 uM JUG C10 H6 O3 c1cc2c(c(c....
5 3DP3 ic50 = 1.52 uM 4BB C18 H18 Br2 N2 O3 CC(C)(C)c1....
6 3DP2 ic50 = 1.5 uM 4BE C14 H9 Br3 N2 O3 c1cc(ccc1C....
7 3DP1 ic50 = 9.92 uM 2RB C15 H12 Br2 N2 O4 COc1ccc(cc....
8 3D04 Ki = 0.9 uM SAK C16 H14 O5 COc1cc(c2c....
9 3DP0 ic50 = 1.42 uM 2BC C18 H12 Br2 N2 O3 c1ccc2cc(c....
10 3DOY ic50 = 1.52 uM 2BE C14 H9 Br2 Cl N2 O3 c1cc(ccc1C....
11 2GLP ic50 = 39.8 uM BDE C13 H9 Br2 N3 O3 c1cc(cnc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EMO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 EMO 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3D04; Ligand: SAK; Similar sites found: 3
This union binding pocket(no: 1) in the query (biounit: 3d04.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3BJK CIT 0.003925 0.41076 1.96078
2 5NJI 8Z2 0.003657 0.40516 4.40252
3 1WN3 HXC 0.003401 0.40778 16.1765
Pocket No.: 2; Query (leader) PDB : 3D04; Ligand: SAK; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3d04.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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