Receptor
PDB id Resolution Class Description Source Keywords
4K10 2.3 Å EC: 2.5.1.10 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:404;
B:404;
C:403;
D:403;
A:405;
B:403;
C:404;
D:404;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
ACT D:402;
B:402;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
PEG A:407;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
NA C:402;
A:401;
B:401;
A:402;
C:401;
A:403;
Invalid;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
NI9 A:406;
B:405;
D:405;
C:405;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 119.5 nM
302.111 C7 H11 F N O7 P2 c1cc(...
MES D:401;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K10 2.3 Å EC: 2.5.1.10 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 (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
2 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
3 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
4 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
5 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
6 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
7 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
8 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
9 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
10 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
11 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
12 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
13 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
14 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
15 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
16 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
17 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
18 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
19 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
20 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
21 3IBA - SO4 O4 S [O-]S(=O)(....
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
4 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
5 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
6 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
7 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
8 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
9 5JV2 ic50 = 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
10 3N5J ic50 = 8 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
11 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
12 3N45 - PO4 O4 P [O-]P(=O)(....
13 4LPH ic50 = 4.5 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
14 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
15 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
16 4LPG ic50 = 0.022 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
17 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
18 3N6K ic50 = 0.2 uM BFH C15 H11 N O4 c1ccc2c(c1....
19 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
20 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
22 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
24 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
25 3N46 - PO4 O4 P [O-]P(=O)(....
26 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
27 4H5C - PO4 O4 P [O-]P(=O)(....
28 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
29 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
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 2O1O Ki = 0.38 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
35 2Q58 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
36 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
37 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
38 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
39 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
40 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
41 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
42 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
43 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
44 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
45 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
46 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
47 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
48 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
49 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
50 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
51 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
52 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
53 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
54 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
55 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
56 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
57 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
58 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
59 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
60 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
61 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
62 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
63 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NI9; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NI9 1 1
2 P2H 0.518519 0.867925
3 364 0.444444 0.867925
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4K10; Ligand: NI9; Similar sites found: 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 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4K10; Ligand: NI9; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 4k10.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OV6 MK0 0.03852 0.41027 1.38122
2 1SR7 MOF 0.03456 0.4075 1.9305
3 1N20 3AG 0.02084 0.41517 1.9337
4 2B9W FAD 0.04232 0.41597 2.48619
5 4O8O AHR 0.01165 0.41515 2.48619
6 3NBK PNS 0.02576 0.40155 3.9548
7 1Q3Q ANP 0.03321 0.40972 4.69613
8 4P6X HCY 0.02352 0.40213 5.4902
9 1UJ2 C5P 0.02617 0.41364 5.55556
10 3V1V GST 0.01244 0.40962 5.80111
11 2NTK IMP 0.00518 0.43485 5.85586
12 4TQ3 GPP 0.006389 0.42676 7.59076
13 2Z7I 742 0.00007445 0.57908 12.0588
Pocket No.: 3; Query (leader) PDB : 4K10; Ligand: NI9; Similar sites found: 10
This union binding pocket(no: 3) in the query (biounit: 4k10.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BC5 SAH 0.03216 0.40111 2.60223
2 2E2R 2OH 0.01919 0.43018 2.86885
3 1MDC PLM 0.0165 0.4015 4.54545
4 5UV1 0FV 0.01883 0.40185 4.69613
5 1CZA ADP 0.01689 0.40297 5.24862
6 3T03 3T0 0.01321 0.41546 5.98592
7 4C3Y FAD 0.03272 0.41379 8.56354
8 1T0I FMN 0.01316 0.41699 12.5654
9 1ELR ACE MET GLU GLU VAL ASP 0.01942 0.40396 16.7939
10 1ID0 ANP 0.001531 0.45114 17.7632
Pocket No.: 4; Query (leader) PDB : 4K10; Ligand: NI9; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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