Receptor
PDB id Resolution Class Description Source Keywords
5HN7 2.15 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOS SYNTHASE COMPLEXED WITH BPH-1158 PLASMODIUM VIVAX TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DYNAMIC STRUCTURE AND INHIBITION OF A MALARIA DRUG GERANYLGERANYL DIPHOSPHATE SYNTHASE. BIOCHEMISTRY V. 55 5180 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
04M B:401;
A:401;
F:401;
D:401;
E:401;
H:401;
G:401;
C:401;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
ic50 = 120 uM
505.624 C26 H35 N O7 S CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3LDW 2.47 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOS SYNTHASE PVX_092040 WITH ZOLEDRONATE AND IPP BOUND PLASMODIUM VIVAX MALARIA FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE LYASESTRUCTURAL GENOMICS ISOPRENE BIOSYNTHESIS TRANSFERASE STGENOMICS CONSORTIUM SGC
Ref.: MOLECULAR CHARACTERIZATION OF A NOVEL GERANYLGERANY PYROPHOSPHATE SYNTHASE FROM PLASMODIUM PARASITES. J.BIOL.CHEM. V. 286 3315 2011
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
3 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
4 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
3 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
4 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
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: 04M; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 04M 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3LDW; Ligand: IPE; 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: 3ldw.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3LDW; Ligand: ZOL; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3ldw.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3LDW; Ligand: IPE; Similar sites found: 27
This union binding pocket(no: 3) in the query (biounit: 3ldw.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YRX FMN 0.009834 0.41186 2.47934
2 2AEL SAZ 0.001109 0.4474 2.6738
3 5UC9 MYR 0.0233 0.4086 3.09735
4 4MLN ODV 0.02884 0.40785 3.57143
5 4Q0A 4OA 0.00825 0.40849 3.97351
6 3B6C SDN 0.00185 0.47068 4.70085
7 4KWD JF2 0.001494 0.41049 4.77707
8 2ZCQ B65 0.0111 0.40022 4.77816
9 3DBX PLM 0.01815 0.40636 5.05051
10 4JIE BMA 0.03995 0.40494 5.05051
11 4MGA 27L 0.04564 0.40408 5.4902
12 5EE7 5MV 0.03522 0.40538 5.53097
13 2C3Q GTX 0.00689 0.42695 6.07287
14 5OCA 9QZ 0.007287 0.45635 7.56302
15 1RQJ RIS 0.000000009522 0.60444 8.3612
16 1RTW MP5 0.008156 0.43684 8.63636
17 4RJD TFP 0.02265 0.41312 9.09091
18 4W4S B29 0.00129 0.43314 10
19 5CX8 RP3 0.01893 0.42351 12.8788
20 5LWY OLB 0.01427 0.40779 13.0841
21 3DGY 2GP 0.02208 0.41584 16.4948
22 3WJO IPE 0.000001526 0.64091 30.8605
23 2Z7I 742 0.000001542 0.58463 31.7647
24 3KRO IPE 0.0000000392 0.5892 37.9661
25 3KRO DST 0.0000000392 0.5892 37.9661
26 3KRO PPV 0.0001564 0.41425 37.9661
27 1YHM AHD 0.00000007281 0.70158 46.4088
Pocket No.: 4; Query (leader) PDB : 3LDW; Ligand: ZOL; Similar sites found: 63
This union binding pocket(no: 4) in the query (biounit: 3ldw.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.01707 0.43467 None
2 2BYC FMN 0.007704 0.42591 None
3 1J78 OLA 0.04076 0.40426 1.51515
4 3OKI OKI 0.01398 0.40033 2.14592
5 4J6C STR 0.04273 0.40349 2.27273
6 1N20 3AG 0.009872 0.4012 2.27273
7 4WGF HX2 0.03872 0.40224 2.43902
8 1YRX FMN 0.008652 0.41974 2.47934
9 1XM4 PIL 0.01356 0.4177 2.52525
10 5K7H IVC 0.01069 0.40256 2.5974
11 3G58 988 0.01161 0.42509 2.62467
12 2AEL SAZ 0.001378 0.4491 2.6738
13 5LX9 OLB 0.02348 0.40236 2.9316
14 5UC9 MYR 0.03009 0.40771 3.09735
15 1TV5 N8E 0.01218 0.43344 3.28283
16 1ID0 ANP 0.02315 0.40612 3.28947
17 5DKK FMN 0.008741 0.41265 3.44828
18 4MLN ODV 0.0355 0.40785 3.57143
19 3W54 RNB 0.0134 0.40738 3.64742
20 4OKZ 3E9 0.000676 0.40086 3.83562
21 4Q0A 4OA 0.009169 0.41171 3.97351
22 3TDC 0EU 0.0003521 0.4917 4.0404
23 5TWO 7MV 0.008719 0.4095 4.41176
24 4V1T ADP 0.01875 0.40057 4.6875
25 3B6C SDN 0.01211 0.43296 4.70085
26 1DKF BMS 0.002647 0.4257 4.72103
27 4KWD JF2 0.0004512 0.41189 4.77707
28 2ZCQ B65 0.004387 0.40704 4.77816
29 3SDV 911 0.005454 0.43319 5.05051
30 3DBX PLM 0.02289 0.40636 5.05051
31 4JIE BMA 0.04836 0.40494 5.05051
32 4MG9 27K 0.01529 0.42755 5.4902
33 4MGA 27L 0.03456 0.41375 5.4902
34 5EE7 5MV 0.01968 0.41985 5.53097
35 2BJ4 OHT 0.004341 0.423 5.55556
36 1K7L 544 0.004511 0.40703 5.90278
37 3SP6 IL2 0.005798 0.42076 5.96491
38 5UNJ RJW 0.0188 0.40371 6.12245
39 4JX1 CAM 0.02651 0.41278 6.19469
40 2NPA MMB 0.01191 0.40051 6.2963
41 1NHZ 486 0.01309 0.40162 6.78571
42 1X0P FAD 0.008549 0.42372 6.99301
43 5OCA 9QZ 0.0007428 0.50716 7.56302
44 2PRG BRL 0.01323 0.40762 7.95455
45 1RQJ RIS 0.00000000003468 0.64565 8.3612
46 1RTW MP5 0.01025 0.43684 8.63636
47 4I67 G G G RPC 0.02156 0.41137 9.1954
48 4V3I ASP LEU THR ARG PRO 0.04896 0.40119 9.33852
49 1LNX URI 0.01962 0.42463 9.87654
50 4W4S B29 0.001531 0.43589 10
51 4UYG 73B 0.01769 0.42415 10.1911
52 4OAS 2SW 0.008272 0.42441 12.5
53 2HFN FMN 0.008664 0.41619 13.0719
54 5LWY OLB 0.008797 0.42312 13.0841
55 3IX9 MTX 0.02071 0.40853 14.7368
56 3SE5 ANP 0.01516 0.40816 15.8537
57 4LWU 20U 0.009353 0.42183 20
58 3WJO IPE 0.000002133 0.64091 30.8605
59 2Z7I 742 0.00000007503 0.61981 31.7647
60 3KRO IPE 0.000000001258 0.60351 37.9661
61 3KRO DST 0.000000001258 0.60351 37.9661
62 3KRO PPV 0.00004633 0.41207 37.9661
63 1YHM AHD 0.00000000006781 0.87195 46.4088
Pocket No.: 5; Query (leader) PDB : 3LDW; Ligand: ZOL; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3ldw.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3LDW; Ligand: IPE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3ldw.bio2) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3LDW; Ligand: IPE; Similar sites found: 10
This union binding pocket(no: 7) in the query (biounit: 3ldw.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.001728 0.482 None
2 2X8S AHR AHR AHR 0.02116 0.41499 2.52525
3 5B0I BOG 0.01001 0.41903 2.62391
4 1GNI OLA 0.01871 0.43899 2.77778
5 5LX9 OLB 0.005426 0.42785 2.9316
6 3B9Z CO2 0.01308 0.42616 3.09278
7 3TDC 0EU 0.01744 0.45178 4.0404
8 4RW3 TDA 0.004947 0.42557 5.29801
9 3LE7 ADE 0.02316 0.41351 6.89655
10 4UCC ZKW 0.04897 0.40535 9.01288
Pocket No.: 8; Query (leader) PDB : 3LDW; Ligand: ZOL; Similar sites found: 7
This union binding pocket(no: 8) in the query (biounit: 3ldw.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5B0I BOG 0.01067 0.41903 2.62391
2 3UPY FOM 0.01759 0.41557 3.0303
3 3B9Z CO2 0.004987 0.46194 3.09278
4 5BRP PNG 0.01315 0.43365 3.78788
5 4RW3 TDA 0.0052 0.42557 5.29801
6 4WO4 JLS 0.00694 0.40334 6.12245
7 4UMJ BFQ 0.0000001414 0.40011 35.473
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