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Receptor
PDB id Resolution Class Description Source Keywords
3V66 1.8 Å EC: 2.5.1.21 HUMAN SQUALENE SYNTHASE IN COMPLEX WITH 2-(1-{2-[(4R,6S)-8-C (2,3-DIMETHOXYPHENYL)-4H,6H-PYRROLO[1,2-A][4,1]BENZOXAZEPINY L]ACETYL}-4-PIPERIDINYL)ACETIC ACID HOMO SAPIENS TERPENOID SYNTHASE FOLD ISOPRENE BIOSYNTHESIS LIPID SYNTHEMULTIFUNCTIONAL ENZYME OXIDOREDUCTASE STEROID BIOSYNTHESIBIOSYNTHESIS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DISCOVERY OF NOVEL TRICYCLIC COMPOUNDS AS SQUALENE INHIBITORS BIOORG.MED.CHEM. V. 20 3072 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
D3A A:402;
Valid;
none;
ic50 = 1.3 nM
539.019 C29 H31 Cl N2 O6 COc1c...
PO4 A:401;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3V66 1.8 Å EC: 2.5.1.21 HUMAN SQUALENE SYNTHASE IN COMPLEX WITH 2-(1-{2-[(4R,6S)-8-C (2,3-DIMETHOXYPHENYL)-4H,6H-PYRROLO[1,2-A][4,1]BENZOXAZEPINY L]ACETYL}-4-PIPERIDINYL)ACETIC ACID HOMO SAPIENS TERPENOID SYNTHASE FOLD ISOPRENE BIOSYNTHESIS LIPID SYNTHEMULTIFUNCTIONAL ENZYME OXIDOREDUCTASE STEROID BIOSYNTHESIBIOSYNTHESIS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DISCOVERY OF NOVEL TRICYCLIC COMPOUNDS AS SQUALENE INHIBITORS BIOORG.MED.CHEM. V. 20 3072 2012
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3WCF ic50 = 0.053 uM BH8 C15 H30 N2 O6 P2 CCCCCCCCCC....
2 1EZF - IN0 C30 H31 Cl N2 O7 CC(C)(C)CN....
3 3Q2Z - D9A C28 H33 Cl N2 O9 CC(C)(C)CN....
4 3ASX ic50 = 20 nM D99 C28 H34 Cl2 N2 O5 CC(C)(C)CN....
5 3WCH ic50 = 0.089 uM 8PH C15 H30 N2 O7 P2 CCCCCCCCCC....
6 3Q30 - D61 C36 H41 N O7 c1ccc2cc(c....
7 3V66 ic50 = 1.3 nM D3A C29 H31 Cl N2 O6 COc1cccc(c....
8 3WCM - ER4 C25 H30 N2 O3 COCCCOc1cc....
9 3WCJ - E5S C26 H31 N3 O3 CO[C@H]1CN....
10 3WCI ic50 = 0.27 uM BH5 C20 H40 N2 O7 P2 CCCCCCCCCC....
11 3WCL ic50 = 0.26 uM BH3 C20 H40 N2 O6 P2 CCCCCCCCCC....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3WCF ic50 = 0.053 uM BH8 C15 H30 N2 O6 P2 CCCCCCCCCC....
2 1EZF - IN0 C30 H31 Cl N2 O7 CC(C)(C)CN....
3 3Q2Z - D9A C28 H33 Cl N2 O9 CC(C)(C)CN....
4 3ASX ic50 = 20 nM D99 C28 H34 Cl2 N2 O5 CC(C)(C)CN....
5 3WCH ic50 = 0.089 uM 8PH C15 H30 N2 O7 P2 CCCCCCCCCC....
6 3Q30 - D61 C36 H41 N O7 c1ccc2cc(c....
7 3V66 ic50 = 1.3 nM D3A C29 H31 Cl N2 O6 COc1cccc(c....
8 3WCM - ER4 C25 H30 N2 O3 COCCCOc1cc....
9 3WCJ - E5S C26 H31 N3 O3 CO[C@H]1CN....
10 3WCI ic50 = 0.27 uM BH5 C20 H40 N2 O7 P2 CCCCCCCCCC....
11 3WCL ic50 = 0.26 uM BH3 C20 H40 N2 O6 P2 CCCCCCCCCC....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3WCC - E5S C26 H31 N3 O3 CO[C@H]1CN....
2 3WCA - FPS C15 H28 O6 P2 S CC(=CCC/C(....
3 3WCF ic50 = 0.053 uM BH8 C15 H30 N2 O6 P2 CCCCCCCCCC....
4 1EZF - IN0 C30 H31 Cl N2 O7 CC(C)(C)CN....
5 3Q2Z - D9A C28 H33 Cl N2 O9 CC(C)(C)CN....
6 3ASX ic50 = 20 nM D99 C28 H34 Cl2 N2 O5 CC(C)(C)CN....
7 3WCH ic50 = 0.089 uM 8PH C15 H30 N2 O7 P2 CCCCCCCCCC....
8 3Q30 - D61 C36 H41 N O7 c1ccc2cc(c....
9 3V66 ic50 = 1.3 nM D3A C29 H31 Cl N2 O6 COc1cccc(c....
10 3WCM - ER4 C25 H30 N2 O3 COCCCOc1cc....
11 3WCJ - E5S C26 H31 N3 O3 CO[C@H]1CN....
12 3WCI ic50 = 0.27 uM BH5 C20 H40 N2 O7 P2 CCCCCCCCCC....
13 3WCL ic50 = 0.26 uM BH3 C20 H40 N2 O6 P2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: D3A; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 D3A 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3V66; Ligand: D3A; Similar sites found with APoc: 312
This union binding pocket(no: 1) in the query (biounit: 3v66.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1UO5 PIH None
3 1NU4 MLA None
4 1BWO LPC None
5 6CS9 PIO None
6 5MTE BB2 None
7 1UO4 PIH None
8 1MID LAP None
9 2ALG DAO None
10 2ALG HP6 None
11 1Q1Y BB2 None
12 3UST FAD 1.1236
13 2Q89 6CS 1.16732
14 4F06 PHB 1.17647
15 1DZK PRZ 1.27389
16 2AEL SAZ 1.47059
17 4LHM AZZ 1.47059
18 6BMS POV 1.47059
19 1C3X 8IG 1.50376
20 2UYQ SAM 1.6129
21 3N7S 3N7 1.73913
22 4OOE FOM 1.76471
23 5Z21 OXM 1.76471
24 4FBL SPD 1.77936
25 3V1S 0LH 1.86335
26 5DX3 EST 1.91571
27 5DXG EST 1.91571
28 5WGQ EST 1.91571
29 5DXE EST 1.91571
30 2QZO KN1 1.93798
31 5HYR EST 1.93798
32 4MG9 27K 1.96078
33 4MGA 27L 1.96078
34 4MGB XDH 1.96078
35 4MGD 27N 1.96078
36 2BJ4 OHT 1.98413
37 4TV1 36M 1.99203
38 3UUA 0CZ 1.99203
39 3UUD EST 1.99203
40 6H8S FSZ 1.99336
41 2HHP FLC 2.05882
42 3X01 AMP 2.05882
43 6C1R EFD 2.05882
44 1XMY ROL 2.05882
45 1XM4 PIL 2.05882
46 2YOO K2B 2.05882
47 6BLD DXJ 2.05882
48 5V3Y 5V8 2.0979
49 5UGW GSH 2.28571
50 3WQM B29 2.32558
51 5H5O PCG 2.32558
52 5KD8 TNR 2.35294
53 4P6X HCY 2.35294
54 5WIU AQD 2.35294
55 3P5P A3C 2.35294
56 3GQT UFO 2.35294
57 2VDY HCY 2.35294
58 3ETG GTP 2.35294
59 3A51 VDY 2.35294
60 3I4X DST 2.35294
61 4H9T HL4 2.42424
62 5Y79 3PG 2.43161
63 1KUK PCA LYS TRP 2.46305
64 2BP1 FLC 2.5
65 3KPX CZH 2.52525
66 4U0S ADP 2.64706
67 4DXJ 0M9 2.64706
68 5OSW DIU 2.64706
69 1I0B PEL 2.71084
70 3W54 RNB 2.73556
71 1NHZ 486 2.85714
72 1A8S PPI 2.9304
73 5CX6 CDP 2.94118
74 2Z9V PXM 2.94118
75 5IKH 6BW 2.94118
76 5VRH OLB 2.94118
77 4OIC A8S 2.94118
78 2FDW D3G 2.94118
79 5ZKC 3C0 2.94118
80 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 2.95082
81 5L7G 6QE 2.95082
82 5MWY YNU 2.95082
83 6AP6 TLF 2.97398
84 1M2Z BOG 3.11284
85 1M2Z DEX 3.11284
86 4V1T ADP 3.125
87 3R9V DXC 3.14685
88 4E2J MOF 3.2
89 1PU7 39A 3.21101
90 3GN8 DEX 3.21285
91 5UFS 1TA 3.22581
92 2W90 6PG 3.23529
93 2E9L PLM 3.23529
94 5EY0 GTP 3.28467
95 4UDB CV7 3.30882
96 4UNR QZE 3.33333
97 2GWH PCI 3.3557
98 3IGZ 2PG 3.38681
99 3IGZ 3PG 3.38681
100 5HCV 60R 3.50195
101 2BIF BOG 3.52941
102 1Q7E MET 3.52941
103 3RS8 ALA TRP LEU PHE GLU ALA 3.52941
104 4KIB SAH 3.52941
105 2Z7I 742 3.52941
106 1MT1 AG2 3.53982
107 2A3I C0R 3.55731
108 2CIX CEJ 3.67893
109 2QJY UQ2 3.71747
110 1DDU CB3 3.77358
111 2PX6 DH9 3.79747
112 4DE3 DN8 3.80228
113 6CDZ CB3 3.80228
114 5K53 STE 3.81679
115 5IM3 DTP 3.82353
116 5UV1 0FV 3.82353
117 5IKR ID8 3.82353
118 4CIB 7UZ 3.82353
119 3KB9 BTM 3.82353
120 6B21 C9V 3.82353
121 2BCG GER 3.8835
122 1CX4 CMP 3.93443
123 5C1M OLC 4
124 5C1M CLR 4
125 4ETZ C2E 4.0404
126 4EXO PYR 4.10959
127 1ZED PNP 4.11765
128 6B04 C6J 4.11765
129 3AI3 SOE 4.18251
130 4RHP PEF 4.25532
131 3E70 GDP 4.26829
132 4TQ3 GPP 4.29043
133 6FS0 E4W 4.40252
134 1P1M MET 4.41176
135 2GBB CIT 4.48718
136 5XJD 87L 4.54545
137 4JE7 BB2 4.56853
138 5LX9 OLB 4.57746
139 3V1V GST 4.61894
140 4V1F BQ1 4.65116
141 2JC9 ADN 4.70588
142 3JRX S1A 4.70588
143 1ZGA HMK 4.70588
144 1W96 S1A 4.70588
145 4GBD MCF 4.70588
146 1O98 2PG 4.70588
147 1N20 3AG 4.70588
148 2OCI TYC 4.72441
149 2F7A BEZ 4.74138
150 3WJO IPE 4.74777
151 5C8W PCG 4.8951
152 4R29 SAM 4.91071
153 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 4.91803
154 1Q19 SSC 5
155 6BR9 PGV 5
156 2O1O RIS 5
157 5IUY BOG 5
158 6BR9 6OU 5
159 2RH1 CLR 5
160 1ZPD CIT 5
161 4DS8 A8S 5
162 3WMX THR 5.02793
163 5JO1 6LM 5.07463
164 5A4W QCT 5.18868
165 5CWA 0GA 5.26316
166 4I90 CHT 5.28053
167 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 5.29412
168 3SDV 911 5.29412
169 3DTU DXC 5.29412
170 1E4I NFG 5.29412
171 2Q8G AZX 5.29412
172 2AK3 AMP 5.30973
173 5UC1 486 5.40541
174 1UKZ AMP 5.41872
175 1OW4 2AN 5.42636
176 5TVI MYR 5.43478
177 5TVI O8N 5.43478
178 2VSS ACO 5.43478
179 2VSU ACO 5.45455
180 4AIG FLX 5.47264
181 3O01 DXC 5.51948
182 3G58 988 5.58824
183 5CKS 52L 5.58824
184 5D4V YGP 5.59701
185 5XQL C2E 5.84192
186 5CX8 RP3 5.88235
187 3CF6 SP1 5.88235
188 3KO0 TFP 5.94059
189 2OKL BB2 5.94595
190 1UUY PPI 5.98802
191 2Q1H AS4 6
192 4RZB NFQ 6.17647
193 6GMN F4E 6.18557
194 4OGQ 7PH 6.25
195 4OGQ 1O2 6.25
196 4OGQ 2WD 6.25
197 3ROE THM 6.41509
198 1DKF OLA 6.43777
199 5MOB A8S 6.46552
200 3NMV PYV 6.48148
201 5Y02 HBX 6.54206
202 3KP6 SAL 6.62252
203 2FP2 TSA 6.62651
204 5G3Y ADP 6.63717
205 3B1M KRC 6.71378
206 2HFP NSI 6.73759
207 6BR8 PGV 6.74603
208 4K10 NI9 6.76471
209 4JZB P2H 6.76471
210 3OF1 CMP 6.91057
211 1FM9 9CR 6.98529
212 4W4S B29 7
213 1RV1 IMZ 7.05882
214 4QO5 NAG 7.05882
215 4B1V LAB 7.05882
216 1J78 OLA 7.05882
217 2UW1 GVM 7.10059
218 3PNA CMP 7.14286
219 3FAL REA 7.14286
220 2IDO TMP 7.22892
221 4UCC ZKW 7.29614
222 3SE5 ANP 7.31707
223 3JSX CC2 7.32601
224 5AZC PGT 7.33333
225 5OLK DTP 7.35294
226 5X5M 7YU 7.40741
227 5X13 HC4 7.44681
228 3TL1 JRO 7.54717
229 2AAZ CB3 7.57098
230 4A69 I0P 7.64706
231 4JHG ZEA 7.7381
232 5UNJ RJW 7.7551
233 1ZDU P3A 7.7551
234 4O4Z N2O 7.79221
235 1YYE 196 7.83582
236 5KBF CMP 7.97342
237 5CHR 4NC 8.0292
238 5C9J DAO 8.08081
239 1NF8 BOG 8.21256
240 5DCH 1YO 8.33333
241 4HBM 0Y7 8.33333
242 4OFG PCG 8.33333
243 4UMJ BFQ 8.44595
244 6AP8 BNY 8.55019
245 3AQT RCO 8.57143
246 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 8.57143
247 3ZCB ATP 8.58586
248 2YJD YJD 8.75
249 4J26 EST 8.75
250 4J24 EST 8.75
251 4MA7 P2Z 8.77193
252 2VWA PTY 8.91089
253 5KAU RHQ 9.09091
254 5MN0 A8S 9.09091
255 3F8C HT1 9.52381
256 3JRS A8S 9.61539
257 6A5Y 9CR 9.64912
258 1XZ3 ICF 9.77011
259 4WQ2 3SU 9.82659
260 4ZGM 32M 9.83607
261 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 9.86842
262 5MWE TCE 9.87654
263 3KDJ A8S 9.90099
264 3SQP 3J8 10
265 1JF0 CZH 10.2564
266 3GF2 SAL 10.274
267 2V0U FMN 10.274
268 5F74 AMP 10.5691
269 3RLF MAL 10.5882
270 1LQY BB2 10.8696
271 5W7B MYR 10.8824
272 5JF2 SF7 11.2745
273 5M37 9SZ 11.3043
274 5TPU TYD 11.5108
275 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 11.7391
276 4KU7 PCG 11.7647
277 4F4S EFO 11.8421
278 3RY9 1CA 12
279 5LWY OLB 12.1495
280 5LWY OLA 12.1495
281 4GCZ FMN 12.6471
282 6CGN DA 13.2353
283 4RYV ZEA 13.5484
284 5V4R MGT 13.5802
285 1UHK CZN 13.6126
286 2Y69 CHD 13.8158
287 5WHU SIA 14.094
288 5WHU SIA GAL GLC 14.094
289 6CAY ERG 14.2012
290 3RV5 DXC 14.6067
291 4V2O CLQ 14.6341
292 1R6N 434 14.6919
293 5OCA 9QZ 15.0794
294 3NY4 SMX 15.4717
295 5M36 9SZ 15.7895
296 1SQK LAR 16
297 3OGN 3OG 16.9355
298 2XN3 ID8 17.5
299 2WOR 2AN 18
300 4WGF HX2 18.5366
301 5URY PAM 19.1781
302 5W97 CHD 19.2661
303 5ZCO CHD 19.2661
304 5Z84 CHD 19.2661
305 5ZCO PEK 19.2661
306 5ZCO PGV 19.2661
307 5SVV FMN 20.438
308 3SQG COM 21.147
309 1SR7 MOF 22.3938
310 4OAR 2S0 22.4806
311 2ZCQ B65 31.058
312 1TW4 CHD 33.6
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