Receptor
PDB id Resolution Class Description Source Keywords
3EGT 2 Å EC: 2.5.1.10 T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE BPH-722 TRYPANOSOMA BRUCEI PROTEIN-BISPHOSPHONATE COMPLEX ISOPRENE BIOSYNTHESIS TRANSFERASE
Ref.: LIPOPHILIC BISPHOSPHONATES AS DUAL FARNESYL/GERANYLGERANYL DIPHOSPHATE SYNTHASE INHIBITORS: AN X-RAY AND NMR INVESTIGATION. J.AM.CHEM.SOC. V. 131 5153 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
722 A:3001;
B:4001;
Valid;
Valid;
none;
none;
Ki = 32 nM
382.306 C14 H26 N O7 P2 CCCCC...
MG A:3002;
A:3003;
A:3004;
B:4002;
B:4003;
B:4004;
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
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2P1C 2.45 Å EC: 2.5.1.10 T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPH BPH-210 TRYPANOSOMA BRUCEI PROTEIN-BISPHOSPHONATE COMPLEX TRANSFERASE
Ref.: STRUCTURES OF A POTENT PHENYLALKYL BISPHOSPHONATE I BOUND TO FARNESYL AND GERANYLGERANYL DIPHOSPHATE SY PROTEINS V. 73 431 2008
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
2 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
3 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
4 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
5 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
6 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
7 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
8 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
9 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
10 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
11 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
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: 722; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 722 1 1
2 714 0.982143 1
3 B71 0.982143 1
4 721 0.810345 0.932203
5 H86 0.493827 0.893939
6 476 0.470588 0.79661
7 PB6 0.422535 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2P1C; Ligand: GG3; Similar sites found: 112
This union binding pocket(no: 1) in the query (biounit: 2p1c.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ALG DAO 0.03795 0.4039 None
2 2VK2 GZL 0.02852 0.41073 1.30719
3 3O0W MAN MAN MAN GLC 0.0309 0.40101 1.4652
4 5V3Y 5V8 0.004462 0.44351 1.74825
5 4IA6 EIC 0.0009289 0.49791 1.79487
6 3HYW DCQ 0.03658 0.40092 1.79487
7 3KU0 ADE 0.02562 0.41981 1.99203
8 3SDV 911 0.007578 0.42369 2.05128
9 3SP6 IL2 0.004164 0.42462 2.10526
10 3KDU NKS 0.006062 0.4098 2.16606
11 4YEF 4CQ 0.03949 0.40303 2.24719
12 3W54 RNB 0.01197 0.40715 2.43161
13 4CT7 TRP 0.0447 0.40384 2.46914
14 4KWD JF2 0.0008171 0.43751 2.54777
15 5FPN KYD 0.01499 0.42722 2.5641
16 2XN5 FUN 0.02207 0.40845 2.57143
17 5GUE GGS 0.002816 0.42515 2.71903
18 4JLZ UTP 0.03847 0.40441 2.82051
19 5UNJ RJW 0.01002 0.41419 2.85714
20 2YJD YJD 0.01869 0.4014 2.91667
21 2WPX ACO 0.01428 0.40046 2.94985
22 4UCC ZKW 0.02546 0.42377 3.00429
23 2WR1 NAG 0.003952 0.42111 3.07692
24 1NRL SRL 0.007145 0.41077 3.16456
25 2GVV DI9 0.02526 0.41346 3.18471
26 2AEL SAZ 0.009012 0.4095 3.20856
27 2X1L MET 0.02532 0.41608 3.43511
28 5A5D 5LC 0.03168 0.40818 3.46021
29 1XQD DND 0.01401 0.404 3.58974
30 1RTW MP5 0.01165 0.43137 3.63636
31 4QEK GLC 0.00565 0.43556 3.65448
32 4EKQ NPO 0.002201 0.44101 3.74332
33 1DKF BMS 0.0009159 0.44251 3.82979
34 3B6C SDN 0.0007563 0.49421 3.84615
35 4EIL FOL 0.01588 0.40148 3.84615
36 5EE7 5MV 0.04174 0.40137 3.84615
37 4OAR 2S0 0.007312 0.41033 3.87597
38 4ZES MMA 0.006685 0.42094 4.08163
39 3AQT RCO 0.03287 0.40914 4.08163
40 4OKZ 3E9 0.001714 0.43097 4.10256
41 3IX9 MTX 0.01571 0.4017 4.21053
42 3MBG FAD 0.00382 0.40728 4.31655
43 5TVI O8N 0.003595 0.45852 4.34783
44 2BYC FMN 0.007785 0.42711 4.37956
45 1KI6 AHU 0.0328 0.4034 4.53172
46 1TV5 N8E 0.01741 0.42307 4.61538
47 3TVQ DQH 0.04707 0.40007 4.73373
48 1J78 OLA 0.04357 0.40571 4.80349
49 5X20 AOT 0.02585 0.41142 4.80769
50 5FQK 6NT 0.02222 0.41789 4.83271
51 1K7L 544 0.003806 0.4102 4.86111
52 4D1J DGJ 0.03966 0.40016 4.87179
53 4HBM 0Y7 0.01901 0.40441 5
54 5ERM 210 0.04006 0.40027 5.23416
55 3LLZ GAL NGA 0.02421 0.40262 5.26316
56 4NB5 2JT 0.01316 0.40207 5.26316
57 3FAL REA 0.02974 0.40186 5.26316
58 5K53 STE 0.01213 0.4006 5.34351
59 1NHZ 486 0.008469 0.40751 5.35714
60 3OO6 GAL 0.009586 0.43769 5.64103
61 3TDC 0EU 0.001442 0.41753 5.64103
62 4YSX E23 0.004274 0.45444 5.67376
63 5KD8 TNR 0.006679 0.44418 5.89744
64 5MBC FMN 0.003513 0.43561 5.94901
65 5V4R MGT 0.0255 0.41504 6.17284
66 4OAS 2SW 0.007813 0.42305 6.25
67 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.00564 0.45247 6.27615
68 1XZ3 ICF 0.002424 0.48046 6.32184
69 2QES ADE 0.02763 0.41903 6.51341
70 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.03094 0.40098 6.66667
71 4RW3 TDA 0.001105 0.4867 6.95364
72 4RW3 PLM 0.0263 0.42777 6.95364
73 1MT1 AG2 0.04965 0.40079 7.07965
74 5OCA 9QZ 0.006669 0.45466 7.14286
75 3JZ0 APC 0.01753 0.40972 7.31707
76 3KMZ EQO 0.001972 0.41585 7.5188
77 1I0B PEL 0.005762 0.46183 7.53012
78 3ET1 ET1 0.009907 0.40764 7.56014
79 2RKN LP3 0.02028 0.40305 7.79221
80 4WUJ FMN 0.01071 0.40611 8.16327
81 4LWU 20U 0.00818 0.42209 8.23529
82 4WGF HX2 0.01773 0.42345 8.29268
83 2BJ4 OHT 0.001582 0.43969 8.33333
84 4MGA 27L 0.02801 0.4132 8.62745
85 4MG9 27K 0.02736 0.4116 8.62745
86 4TUZ 36J 0.01809 0.40903 8.62745
87 4TV1 36M 0.02976 0.40964 8.76494
88 4I67 G G G RPC 0.005972 0.43714 9.1954
89 4IBF 1D5 0.01033 0.4172 10.0775
90 1EX7 5GP 0.03734 0.40435 10.2151
91 1YRX FMN 0.00306 0.43842 10.7438
92 2Z7I 742 0.000000008361 0.43239 10.8824
93 2F2G HMH 0.01828 0.42402 11.3122
94 2Q4X HMH 0.03582 0.40383 11.3122
95 5TWO 7MV 0.007006 0.41115 12.1324
96 2PRG BRL 0.0104 0.40998 12.1771
97 3JUQ AJD 0.007952 0.40266 12.4324
98 5LX9 OLB 0.006885 0.42569 12.7036
99 3WUR O4B 0.01461 0.41828 12.8655
100 5LWY OLB 0.006464 0.42701 13.3562
101 5MWE TCE 0.04488 0.40004 13.5802
102 4WH9 3M8 0.0213 0.41546 13.6612
103 1ID0 ANP 0.02058 0.40626 13.8158
104 1J1R ADE 0.04617 0.40209 14.1762
105 2CB8 MYA 0.01527 0.42742 14.9425
106 1LNX URI 0.02732 0.41443 16.0494
107 1XVB 3BR 0.009593 0.42676 19.4118
108 2J1P GRG 0.00005532 0.49418 23.8908
109 3WJO IPE 0.000267 0.52519 24.0356
110 3KRO IPE 0.00000001713 0.62181 28.4746
111 3KRO DST 0.00000001713 0.62181 28.4746
112 3KRO PPV 0.003329 0.44086 28.4746
Pocket No.: 2; Query (leader) PDB : 2P1C; Ligand: GG3; 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: 2p1c.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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