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 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: EMO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 EMO 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: EMO; Similar ligands found: 175
No: Ligand Similarity coefficient
1 FT2 1.0000
2 LFN 0.9505
3 9TF 0.9501
4 JRO 0.9481
5 NRA 0.9459
6 E1K 0.9453
7 TXQ 0.9419
8 RHN 0.9383
9 MNY 0.9319
10 537 0.9307
11 27M 0.9293
12 LUM 0.9287
13 DPT 0.9233
14 1YL 0.9219
15 PRL 0.9212
16 NOM 0.9200
17 8SK 0.9198
18 ZSP 0.9176
19 3J8 0.9172
20 JTA 0.9170
21 GNV 0.9161
22 H4B 0.9155
23 REF 0.9150
24 DX7 0.9131
25 1DR 0.9126
26 Q0K 0.9111
27 1EL 0.9106
28 HC8 0.9094
29 19E 0.9086
30 2WU 0.9086
31 HNA 0.9073
32 BA5 0.9067
33 XM5 0.9043
34 THA 0.9032
35 S98 0.9022
36 39Z 0.9020
37 113 0.9011
38 CUE 0.9008
39 IQZ 0.8995
40 8MO 0.8995
41 AZN 0.8991
42 CZ0 0.8990
43 JY4 0.8990
44 S60 0.8987
45 HRD 0.8982
46 WS6 0.8977
47 DNQ 0.8964
48 ANC 0.8961
49 272 0.8954
50 6QF 0.8952
51 ANF 0.8952
52 BGU 0.8949
53 AA 0.8941
54 EQU 0.8938
55 HRM 0.8929
56 CNI 0.8913
57 1WO 0.8899
58 FQX 0.8893
59 EST 0.8890
60 18E 0.8881
61 6FB 0.8879
62 MNX 0.8877
63 M3F 0.8875
64 CX6 0.8875
65 5XL 0.8874
66 GNY 0.8873
67 IXM 0.8867
68 AQN 0.8858
69 GNJ 0.8856
70 TIY 0.8855
71 344 0.8853
72 VUP 0.8848
73 UN9 0.8846
74 BIK 0.8841
75 ALR 0.8840
76 B56 0.8827
77 N0Z 0.8827
78 PK3 0.8826
79 5AD 0.8826
80 6TJ 0.8826
81 XTS 0.8820
82 MFR 0.8817
83 30G 0.8815
84 2J1 0.8811
85 ITE 0.8807
86 Z21 0.8806
87 DNA 0.8800
88 K7H 0.8794
89 II4 0.8794
90 2MQ 0.8791
91 ADL 0.8786
92 2K8 0.8779
93 J3Z 0.8776
94 GNM 0.8776
95 9KZ 0.8775
96 5WT 0.8771
97 1TJ 0.8766
98 2AN 0.8766
99 DY9 0.8762
100 OAL 0.8760
101 9CE 0.8751
102 Z73 0.8741
103 NEU 0.8741
104 DRG 0.8738
105 7AP 0.8738
106 5V7 0.8737
107 609 0.8733
108 WS7 0.8732
109 1HN 0.8727
110 TCR 0.8725
111 2JK 0.8724
112 4HG 0.8723
113 SDN 0.8720
114 K44 0.8710
115 E2Q 0.8706
116 HBI 0.8704
117 BIO 0.8702
118 62D 0.8700
119 AN3 0.8692
120 HHS 0.8690
121 FXE 0.8686
122 4AN 0.8686
123 5TY 0.8684
124 1FL 0.8684
125 BRY 0.8680
126 8DA 0.8671
127 3Y7 0.8670
128 H5B 0.8670
129 DK1 0.8668
130 2V4 0.8665
131 CC6 0.8658
132 54X 0.8656
133 4RU 0.8651
134 1V1 0.8651
135 20D 0.8650
136 JF8 0.8648
137 A73 0.8643
138 GJP 0.8643
139 8G6 0.8642
140 X2M 0.8641
141 FNT 0.8641
142 68A 0.8638
143 0FR 0.8630
144 UXH 0.8626
145 WV7 0.8623
146 HH6 0.8620
147 GNG 0.8619
148 AO 0.8619
149 DFL 0.8618
150 MRI 0.8615
151 6VW 0.8614
152 LP8 0.8613
153 IDZ 0.8600
154 JWS 0.8595
155 X0T 0.8594
156 AD3 0.8592
157 0XT 0.8592
158 2GQ 0.8585
159 X0U 0.8582
160 G12 0.8580
161 6ZE 0.8574
162 ZYR 0.8572
163 GRI 0.8570
164 17M 0.8570
165 4KL 0.8564
166 XYP XYP 0.8559
167 DX2 0.8559
168 2FQ 0.8557
169 NEO 0.8557
170 DBQ 0.8553
171 774 0.8547
172 MXX 0.8538
173 3L1 0.8524
174 GA2 0.8521
175 PEY 0.8516
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
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