Receptor
PDB id Resolution Class Description Source Keywords
2GLP 2.42 Å EC: 4.2.1.- CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE(FABZ) FROM HELICOBACTER PYLORI COMPLEXED WITH C HELICOBACTER PYLORI FABZ COMPLEX LYASE
Ref.: STRUCTURAL BASIS FOR CATALYTIC AND INHIBITORY MECHA BETA-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE ( J.BIOL.CHEM. V. 283 5370 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BDE A:3001;
C:3002;
Valid;
Valid;
none;
none;
Ki = 9.7 uM
415.037 C13 H9 Br2 N3 O3 c1cc(...
BEN A:2001;
A:2004;
A:2005;
A:2007;
A:2009;
B:2006;
B:2008;
C:2010;
F:2002;
F:2003;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
120.152 C7 H8 N2 [H]/N...
CL A:1001;
B:1002;
C:1003;
D:1004;
E:1005;
F:1006;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
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 Ki = 9.7 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 Ki = 9.7 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 Ki = 9.7 uM BDE C13 H9 Br2 N3 O3 c1cc(cnc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BDE; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 BDE 1 1
2 3BE 0.626866 0.893617
3 4BE 0.615385 0.893617
4 4BB 0.602941 0.807692
5 2BE 0.597015 0.875
6 2RB 0.57971 0.84
7 2BC 0.561644 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: BDE; Similar ligands found: 83
No: Ligand Similarity coefficient
1 P9L 0.9114
2 9W8 0.9107
3 F91 0.9084
4 T5J 0.9074
5 M62 0.9047
6 1VG 0.9039
7 3K1 0.8972
8 NPZ 0.8961
9 4B8 0.8920
10 EXP 0.8909
11 9ME 0.8898
12 4KN 0.8867
13 K3T 0.8861
14 S16 0.8856
15 5YA 0.8855
16 14X 0.8853
17 1UT 0.8851
18 CMZ 0.8842
19 SCE 0.8841
20 0QX 0.8838
21 97K 0.8832
22 Q2S 0.8832
23 1V0 0.8823
24 BCE 0.8818
25 EMU 0.8816
26 1OX 0.8811
27 5XM 0.8811
28 L02 0.8810
29 4P9 0.8809
30 RF2 0.8807
31 B4L 0.8800
32 68Q 0.8780
33 AU6 0.8780
34 T21 0.8779
35 DX6 0.8774
36 MRE 0.8766
37 51P 0.8755
38 DN8 0.8752
39 5OA 0.8745
40 F38 0.8739
41 3TI 0.8739
42 9M9 0.8731
43 IW5 0.8707
44 IHU 0.8702
45 CWP 0.8701
46 H0V 0.8699
47 0RB 0.8691
48 GJW 0.8682
49 OUA 0.8680
50 OT4 0.8678
51 39R 0.8671
52 EX7 0.8665
53 BFS 0.8663
54 0UC 0.8657
55 SAQ 0.8656
56 NOJ BGC 0.8651
57 E92 0.8650
58 KC8 0.8649
59 41L 0.8647
60 2ZT 0.8639
61 IPJ 0.8639
62 BXZ 0.8638
63 LRT 0.8630
64 334 0.8627
65 M0S 0.8625
66 JZR 0.8622
67 OSY 0.8617
68 M0M 0.8616
69 OUG 0.8611
70 QUE 0.8608
71 1UW 0.8601
72 TRP GLY 0.8598
73 UV4 0.8594
74 5EZ 0.8593
75 6F3 0.8591
76 16V 0.8586
77 MBE 0.8581
78 M16 0.8571
79 BZM 0.8565
80 IW3 0.8563
81 W2E 0.8553
82 1Q2 0.8549
83 NNL 0.8539
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3D04; Ligand: SAK; 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: 3d04.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3D04; Ligand: SAK; 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: 3d04.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback