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: 54
This union binding pocket(no: 1) in the query (biounit: 3v66.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KPE TM3 0.01322 0.429 None
2 1DZK PRZ 0.03424 0.40238 1.27389
3 4OOE FOM 0.03573 0.40145 1.76471
4 4MGD 27N 0.02821 0.40662 1.96078
5 3UUA 0CZ 0.03521 0.40848 1.99203
6 1XM4 PIL 0.0223 0.41523 2.05882
7 2YOO K2B 0.02318 0.40158 2.05882
8 3GQT UFO 0.01749 0.42064 2.35294
9 3KPX CZH 0.007344 0.40736 2.52525
10 2FDW D3G 0.03083 0.41527 2.94118
11 2Z9V PXM 0.04156 0.41209 2.94118
12 1M2Z DEX 0.006527 0.4241 3.11284
13 4E2J MOF 0.009973 0.40976 3.2
14 3GN8 DEX 0.00912 0.41743 3.21285
15 5UFS 1TA 0.01018 0.40936 3.22581
16 4UDB CV7 0.009304 0.40563 3.30882
17 4UNR QZE 0.02031 0.41045 3.33333
18 2Z7I 742 0.003873 0.40881 3.52941
19 2BCG GER 0.01016 0.44112 3.8835
20 2GKL PD2 0.03873 0.40288 3.96476
21 1P1M MET 0.006378 0.41834 4.41176
22 4GBD MCF 0.003073 0.43564 4.70588
23 3JRX S1A 0.007148 0.429 4.70588
24 1O98 2PG 0.02256 0.40821 4.70588
25 2OCI TYC 0.04161 0.41145 4.72441
26 3WJO IPE 0.02061 0.4276 4.74777
27 4R29 SAM 0.04296 0.40391 4.91071
28 4DS8 A8S 0.02252 0.41154 5
29 3WMX THR 0.01218 0.4197 5.02793
30 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.03098 0.42746 5.29412
31 3OF1 CMP 0.03287 0.41005 6.91057
32 4W4S B29 0.0007525 0.45927 7
33 1J78 OLA 0.01106 0.42251 7.05882
34 4B1V LAB 0.02701 0.41455 7.05882
35 3PNA CMP 0.02509 0.42009 7.14286
36 4UCC ZKW 0.02548 0.41378 7.29614
37 3SE5 ANP 0.008681 0.4285 7.31707
38 3TL1 JRO 0.01606 0.43489 7.54717
39 4A69 I0P 0.0293 0.4205 7.64706
40 3K3K A8S 0.01051 0.41459 8.05687
41 1NF8 BOG 0.007998 0.45714 8.21256
42 5DCH 1YO 0.003202 0.47456 8.33333
43 4OFG PCG 0.03227 0.40698 8.33333
44 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.02933 0.41266 8.57143
45 2VWA PTY 0.01029 0.45329 8.91089
46 2V0U FMN 0.02462 0.40034 10.274
47 1LQY BB2 0.01787 0.40996 10.8696
48 4KU7 PCG 0.02565 0.41211 11.7647
49 4F4S EFO 0.0242 0.42508 11.8421
50 3RY9 1CA 0.02288 0.4048 12
51 5V4R MGT 0.002984 0.49211 13.5802
52 1UHK CZN 0.006335 0.40745 13.6126
53 3OGN 3OG 0.01987 0.40774 16.9355
54 2ZCQ B65 0.00000004358 0.56341 31.058
Feedback