Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BEN A:161;
A:162;
C:161;
E:161;
E:162;
F:161;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
120.152 C7 H8 N2 [H]/N...
CL A:160;
B:160;
C:160;
D:160;
E:160;
F:160;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
SAK A:163;
C:162;
 Valid;
Valid;
 none;
none;
 Ki = 0.9 uM
286.279 C16 H14 O5 COc1c...
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: SAK; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 SAK 1 1
2 CWE 0.65 0.870968
3 NAR 0.65 0.870968
4 6JP 0.479452 0.909091
5 DFV 0.454545 0.866667
6 DFL 0.426471 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: SAK; Similar ligands found: 336
No: Ligand Similarity coefficient
1 6B5 0.9761
2 AGI 0.9690
3 O9Z 0.9690
4 LU2 0.9683
5 O9T 0.9677
6 7LU 0.9650
7 J8G 0.9627
8 KMP 0.9621
9 3JC 0.9576
10 QUE 0.9574
11 J8D 0.9574
12 57D 0.9521
13 3WL 0.9480
14 DDC 0.9467
15 MRI 0.9462
16 OSY 0.9461
17 DQH 0.9430
18 O9Q 0.9426
19 DH2 0.9396
20 FSE 0.9348
21 3TI 0.9334
22 HUL 0.9329
23 6BK 0.9319
24 MYC 0.9316
25 KXN 0.9311
26 DX8 0.9301
27 0H5 0.9301
28 SGW 0.9296
29 AJ6 0.9294
30 28E 0.9293
31 NU3 0.9274
32 H32 0.9253
33 IRH 0.9245
34 HWB 0.9238
35 MYU 0.9236
36 CC6 0.9229
37 EGT 0.9226
38 AX1 0.9220
39 M16 0.9213
40 BJ4 0.9211
41 NKI 0.9204
42 E9L 0.9197
43 AJ4 0.9197
44 A63 0.9192
45 1R5 0.9182
46 5WW 0.9181
47 CDJ 0.9171
48 5DE 0.9171
49 SZ5 0.9158
50 25F 0.9151
51 H2W 0.9148
52 7G2 0.9136
53 1V1 0.9135
54 08C 0.9133
55 3F4 0.9132
56 A73 0.9130
57 20D 0.9122
58 BHF 0.9117
59 W8L 0.9114
60 HCC 0.9096
61 1UZ 0.9095
62 VT3 0.9088
63 6JM 0.9088
64 9K2 0.9084
65 697 0.9083
66 91F 0.9074
67 GKW 0.9074
68 IMK 0.9066
69 M3W 0.9065
70 TH1 0.9057
71 40N 0.9056
72 LZ7 0.9056
73 27F 0.9050
74 BUX 0.9043
75 1V8 0.9042
76 T86 0.9037
77 GQE 0.9030
78 8E3 0.9029
79 D4X 0.9028
80 4L2 0.9025
81 CU5 0.9018
82 3XL 0.9016
83 1UT 0.9011
84 ML1 0.9009
85 A64 0.9002
86 1V0 0.9000
87 15Q 0.8997
88 1Q4 0.8995
89 RGK 0.8992
90 SU9 0.8990
91 B4L 0.8988
92 6XC 0.8988
93 8EC 0.8982
94 1UR 0.8982
95 OUA 0.8981
96 01I 0.8980
97 OUG 0.8973
98 123 0.8972
99 BU7 0.8967
100 Q12 0.8966
101 3GX 0.8966
102 7L4 0.8962
103 L3L 0.8962
104 GOW 0.8959
105 BIT 0.8956
106 8E6 0.8955
107 GQZ 0.8952
108 WLH 0.8951
109 X2L 0.8951
110 553 0.8950
111 797 0.8941
112 NPZ 0.8940
113 7VF 0.8939
114 T34 0.8938
115 5NN 0.8938
116 1HP 0.8935
117 9XZ 0.8934
118 AOB 0.8934
119 3DE 0.8934
120 4YF 0.8933
121 FY8 0.8932
122 F40 0.8929
123 T61 0.8929
124 SNJ 0.8926
125 XZ1 0.8924
126 BRY 0.8921
127 F36 0.8921
128 97K 0.8920
129 25K 0.8915
130 6DQ 0.8906
131 BL7 0.8905
132 BL6 0.8903
133 NYJ 0.8898
134 QS4 0.8895
135 FL9 0.8890
136 4K2 0.8889
137 8HH 0.8885
138 D64 0.8883
139 T5J 0.8875
140 Q11 0.8875
141 IPJ 0.8874
142 6JO 0.8871
143 P4L 0.8867
144 D4O 0.8866
145 GEN 0.8866
146 YL3 0.8865
147 338 0.8863
148 6QX 0.8862
149 76P 0.8861
150 DX7 0.8860
151 ECZ 0.8860
152 334 0.8855
153 K4T 0.8853
154 7FC 0.8852
155 AJ8 0.8852
156 1V4 0.8850
157 G2V 0.8846
158 ML2 0.8843
159 907 0.8839
160 Q92 0.8838
161 TVC 0.8838
162 9CE 0.8834
163 NIF 0.8834
164 6DE 0.8834
165 BZC 0.8832
166 O53 0.8832
167 8M5 0.8832
168 P34 0.8831
169 TYP 0.8828
170 FL8 0.8827
171 3Q0 0.8826
172 1V3 0.8825
173 K8W 0.8825
174 ZRL 0.8825
175 FZB 0.8823
176 MXM 0.8822
177 DN8 0.8820
178 XYP XIM 0.8816
179 LI7 0.8813
180 I0D 0.8812
181 4L6 0.8812
182 X8E 0.8809
183 GT2 0.8807
184 RPB 0.8806
185 TGW 0.8802
186 M08 0.8802
187 EBB 0.8801
188 NW1 0.8798
189 1FL 0.8798
190 JYM 0.8796
191 KS5 0.8795
192 694 0.8793
193 OSJ 0.8792
194 29F 0.8790
195 CMG 0.8790
196 BUN 0.8783
197 X8I 0.8779
198 3WJ 0.8779
199 3RL 0.8778
200 3CA 0.8778
201 D5F 0.8777
202 IDD 0.8775
203 57U 0.8773
204 EEY 0.8772
205 FX5 0.8770
206 0O7 0.8769
207 B7H 0.8767
208 79X 0.8767
209 LVY 0.8766
210 5ZM 0.8763
211 MT6 0.8762
212 QUG 0.8760
213 499 0.8758
214 43O 0.8757
215 3WK 0.8757
216 802 0.8757
217 IW6 0.8751
218 6TJ 0.8749
219 OT4 0.8745
220 1K0 0.8743
221 5KN 0.8741
222 2UV 0.8741
223 196 0.8740
224 F08 0.8740
225 FHI 0.8740
226 HH6 0.8740
227 LJ5 0.8739
228 XYP XYP 0.8733
229 IY5 0.8733
230 UV4 0.8731
231 HWH 0.8730
232 E7E 0.8726
233 0FZ 0.8725
234 4QX 0.8725
235 147 0.8722
236 F13 0.8722
237 6QT 0.8719
238 5E5 0.8719
239 5P3 0.8717
240 2WF 0.8716
241 2QV 0.8716
242 4RV 0.8713
243 E6Q 0.8713
244 43G 0.8713
245 7EH 0.8710
246 68C 0.8710
247 47V 0.8708
248 3Q1 0.8707
249 IK1 0.8706
250 MHB 0.8706
251 BK2 0.8706
252 4CN 0.8705
253 21E 0.8703
254 6FX 0.8703
255 0DF 0.8701
256 SDN 0.8701
257 FO2 0.8689
258 JTF 0.8686
259 DTQ 0.8685
260 5B2 0.8685
261 3G5 0.8678
262 YEX 0.8676
263 TVZ 0.8673
264 E92 0.8672
265 36I 0.8671
266 62D 0.8670
267 STL 0.8668
268 XAV 0.8666
269 DXK 0.8666
270 INR 0.8665
271 LMZ 0.8663
272 J2W 0.8660
273 J2Q 0.8659
274 7M2 0.8658
275 YJX 0.8657
276 OA4 0.8653
277 31F 0.8652
278 KOM 0.8652
279 16L 0.8651
280 4B8 0.8649
281 5YA 0.8642
282 XYS AZI XYS 0.8641
283 108 0.8641
284 AIQ 0.8639
285 WG8 0.8639
286 PIT 0.8637
287 FDZ 0.8635
288 IZ9 0.8635
289 FSU 0.8634
290 4AJ 0.8631
291 X0T 0.8629
292 A3V 0.8627
293 785 0.8627
294 PIQ 0.8624
295 NZ4 0.8617
296 EES 0.8616
297 5XM 0.8615
298 LJ2 0.8614
299 GUS 0.8613
300 5EZ 0.8612
301 4YE 0.8606
302 2QU 0.8603
303 HRD 0.8602
304 ZRK 0.8602
305 YK9 0.8601
306 CFK 0.8600
307 9JT 0.8598
308 W2E 0.8597
309 IYX 0.8597
310 KSF 0.8592
311 ZAR 0.8588
312 TQ1 0.8585
313 T21 0.8583
314 WST 0.8580
315 RF2 0.8579
316 47X 0.8578
317 DZ2 0.8574
318 7M5 0.8573
319 L6Y 0.8572
320 4ZF 0.8570
321 0OP 0.8569
322 Q5M 0.8567
323 R4E 0.8564
324 4YC 0.8560
325 0RA 0.8559
326 L2K 0.8554
327 L43 0.8550
328 IRG 0.8546
329 GRK 0.8544
330 2GQ 0.8542
331 136 0.8538
332 B5T 0.8534
333 53X 0.8533
334 3XM 0.8532
335 FNT 0.8529
336 U4J 0.8520
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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