Receptor
PDB id Resolution Class Description Source Keywords
6WW1 2.05 Å EC: 2.5.1.1 CRYSTAL STRUCTURE OF THE LMFPPS MUTANT E97Y LEISHMANIA MAJOR FPPS FARNESYL DIPHOSPHATE SYNTHASE TRANSFERASE
Ref.: IDENTIFYING STRUCTURAL DETERMINANTS OF PRODUCT SPEC IN LEISHMANIA MAJOR FARNESYL DIPHOSPHATE SYNTHASE. BIOCHEMISTRY V. 59 2751 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:401;
B:402;
A:403;
B:403;
B:401;
A:402;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
476 B:405;
A:405;
 Valid;
Valid;
 none;
none;
 submit data
324.227 C11 H20 N O6 P2 CCCCc...
IPR B:404;
A:404;
 Invalid;
Invalid;
 none;
none;
 submit data
248.108 C5 H14 O7 P2 CC(C)...
ACT B:406;
A:406;
 Invalid;
Invalid;
 none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K10 2.3 Å EC: 2.5.1.1 CRYSTAL STRUCTURE OF LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE IN COMPLEX WITH 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)A ND MG2+ LEISHMANIA MAJOR GERANYL TRANSFERASE FPPS FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE SYNTHASE TRANSFERASE-TRANSFERASE INHIBITOR COM
Ref.: STRUCTURAL AND THERMODYNAMIC BASIS OF THE INHIBITIO LEISHMANIA MAJOR FARNESYL DIPHOSPHATE SYNTHASE BY NITROGEN-CONTAINING BISPHOSPHONATES. ACTA CRYSTALLOGR.,SECT.D V. 70 802 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6WW1 - 476 C11 H20 N O6 P2 CCCCc1ccc[....
2 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6WW1 - 476 C11 H20 N O6 P2 CCCCc1ccc[....
2 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
3 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
4 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
5 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
6 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
7 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
8 3EGT Ki = 1.26 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
9 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
10 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
11 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
12 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
13 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
14 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
15 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
16 3ICK - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
17 4DWB ic50 = 1840 nM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
18 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
19 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
20 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
21 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
22 3IBA - SO4 O4 S [O-]S(=O)(....
50% Homology Family (65)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
4 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
5 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
6 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
7 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
8 3N45 - PO4 O4 P [O-]P(=O)(....
9 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
10 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
11 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
12 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
13 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
14 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
15 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
16 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
17 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
18 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
19 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
20 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
22 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
23 3N46 - PO4 O4 P [O-]P(=O)(....
24 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
25 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
26 4H5C - PO4 O4 P [O-]P(=O)(....
27 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
28 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
29 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
30 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
31 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
32 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
33 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
34 6B07 - C6M C10 H18 N O6 P2 CCC[N]1=C(....
35 6B04 - C6J C8 H14 N O6 P2 C[N]1=C(C=....
36 2Q58 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
37 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
38 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
39 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
40 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
41 6WW1 - 476 C11 H20 N O6 P2 CCCCc1ccc[....
42 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
43 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
44 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
45 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
46 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
47 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
48 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
49 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
50 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
51 3EGT Ki = 1.26 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
52 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
53 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
54 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
55 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
56 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
57 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
58 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
59 3ICK - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
60 4DWB ic50 = 1840 nM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
61 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
62 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
63 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
64 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
65 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 476; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 476 1 1
2 721 0.507937 0.821429
3 PB6 0.491803 0.875
4 722 0.470588 0.79661
5 B71 0.463768 0.79661
6 714 0.463768 0.79661
Similar Ligands (3D)
Ligand no: 1; Ligand: 476; Similar ligands found: 5
No: Ligand Similarity coefficient
1 P2H 0.9253
2 BFQ 0.9068
3 0M8 0.8674
4 M0N 0.8663
5 NI9 0.8629
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4K10; Ligand: NI9; 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: 4k10.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4K10; Ligand: NI9; 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: 4k10.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4K10; Ligand: NI9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4k10.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4K10; Ligand: NI9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4k10.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
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