Receptor
PDB id Resolution Class Description Source Keywords
2Z7I 2.1 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPL INHIBITOR BPH-742 SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE GERANYLGERANYL PYROPHOSPHATE BISPHOSPHONCAROTENOID BIOSYNTHESIS ISOPRENE BIOSYNTHESIS MULTIFUNCTIENZYME PROTEIN TRANSPORT TRANSPORT TRANSFERASE TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: INHIBITION OF GERANYLGERANYL DIPHOSPHATE SYNTHASE B BISPHOSPHONATES: A CRYSTALLOGRAPHIC AND COMPUTATION INVESTIGATION J.MED.CHEM. V. 51 5594 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
742 A:1302;
B:1303;
Valid;
Valid;
none;
none;
ic50 = 0.1 uM
419.391 C16 H38 O6 P3 CCCCC...
MG A:1301;
B:1302;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Z7I 2.1 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPL INHIBITOR BPH-742 SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE GERANYLGERANYL PYROPHOSPHATE BISPHOSPHONCAROTENOID BIOSYNTHESIS ISOPRENE BIOSYNTHESIS MULTIFUNCTIENZYME PROTEIN TRANSPORT TRANSPORT TRANSFERASE TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: INHIBITION OF GERANYLGERANYL DIPHOSPHATE SYNTHASE B BISPHOSPHONATES: A CRYSTALLOGRAPHIC AND COMPUTATION INVESTIGATION J.MED.CHEM. V. 51 5594 2008
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.2 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.2 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.2 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 742; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 742 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Z7I; Ligand: 742; 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: 2z7i.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2Z7I; Ligand: 742; Similar sites found: 157
This union binding pocket(no: 2) in the query (biounit: 2z7i.bio1) has 65 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4W4S B29 0.004363 0.44502 1.66667
2 1TIQ COA 0.04882 0.41111 1.66667
3 4D3S BOG 0.04601 0.40954 1.70648
4 2HHP FLC 0.0002221 0.53405 1.76471
5 4MRP GSH 0.01245 0.46392 1.76471
6 1I0B PEL 0.04168 0.40717 1.80723
7 3AQT RCO 0.03024 0.44077 2.04082
8 5KD8 TNR 0.02408 0.44259 2.05882
9 1VBH PEP 0.03116 0.43793 2.05882
10 3ETG GWD 0.02029 0.42806 2.05882
11 4KCF AKM 0.01335 0.41956 2.05882
12 3W54 RNB 0.04937 0.41085 2.12766
13 5UC9 MYR 0.02648 0.42867 2.21239
14 2J5V PCA 0.0422 0.44191 2.35294
15 1XQD DND 0.04728 0.40612 2.35294
16 3TL1 JRO 0.02338 0.44333 2.51572
17 2OBM ADP 0.03106 0.4411 2.64706
18 5GUE GGS 0.009285 0.43255 2.71903
19 4WUJ FMN 0.03543 0.40978 2.72109
20 3WVS RRM 0.01827 0.41847 2.94118
21 3KO0 TFP 0.03015 0.42592 2.9703
22 2C04 GCP 0.03184 0.41493 3.0303
23 4MGA 27L 0.01543 0.45883 3.13725
24 4TUZ 36J 0.04292 0.41727 3.13725
25 4MG7 27H 0.03796 0.41103 3.13725
26 3ZC7 ATP 0.02305 0.42846 3.14961
27 2BJ4 OHT 0.03981 0.40464 3.1746
28 4KWD JF2 0.005452 0.43467 3.18471
29 4TV1 36M 0.02092 0.44613 3.18725
30 3TDC 0EU 0.0001164 0.62359 3.23529
31 4IA6 EIC 0.001489 0.51862 3.23529
32 2Q8H TF4 0.007965 0.45716 3.23529
33 2WKQ FMN 0.0356 0.40968 3.31325
34 1NF8 BOG 0.009549 0.47202 3.38164
35 3HOK Q80 0.03115 0.42153 3.43348
36 4DZ1 DAL 0.03722 0.43062 3.4749
37 3N7S 3N7 0.03804 0.43374 3.47826
38 2GMH UQ5 0.01943 0.41455 3.52941
39 3V66 D3A 0.003873 0.40881 3.52941
40 3KMZ EQO 0.02325 0.40154 3.52941
41 4IEH 1E9 0.01676 0.41499 3.5503
42 2PIE GLU LEU LYS TPO GLU ARG TYR 0.04425 0.42988 3.62319
43 2BYC FMN 0.03123 0.42147 3.64964
44 2AEL SAZ 0.01362 0.43051 3.82353
45 1BUC CAA 0.02727 0.40285 3.82353
46 3G5K BB2 0.04983 0.40772 3.82514
47 3B6C SDN 0.001857 0.50648 3.84615
48 4F4S EFO 0.02841 0.43842 3.94737
49 2VWA PTY 0.005007 0.49088 3.9604
50 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.01821 0.45593 4.08163
51 2PX6 DH9 0.03629 0.41494 4.11392
52 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.004933 0.4286 4.20168
53 3B9Q MLI 0.0208 0.43156 4.30464
54 3IA4 MTX 0.04377 0.41365 4.32099
55 1Q2C COA 0.03419 0.40292 4.32099
56 5CX6 CDP 0.0434 0.43046 4.41176
57 3SDV 911 0.02841 0.42366 4.41176
58 3FIU POP 0.03267 0.43602 4.41767
59 3QKD HI0 0.0173 0.41692 4.41989
60 4URN NOV 0.04126 0.429 4.44444
61 1XMY ROL 0.01684 0.4472 4.70588
62 1XM4 PIL 0.02059 0.43457 4.70588
63 2YLD CMO 0.03208 0.43966 4.72441
64 2V0U FMN 0.03728 0.40867 4.79452
65 5B4B LP5 0.009441 0.4141 4.83871
66 3OGN 3OG 0.03355 0.41377 4.83871
67 1TV5 N8E 0.02477 0.44188 4.96614
68 5IKH 6BW 0.01374 0.40095 5
69 2PR5 FMN 0.04148 0.40634 5.30303
70 1TMX HGX 0.02528 0.41169 5.46075
71 4XPL ACO 0.008997 0.44278 5.52147
72 5UGW GSH 0.005654 0.46185 5.71429
73 4OIC A8S 0.04975 0.40775 5.7971
74 4ELG 52J 0.03645 0.4016 6.0241
75 4EES FMN 0.04539 0.40182 6.08696
76 2ZCQ B65 0.0006029 0.43202 6.14334
77 3L1N PLM 0.02551 0.44114 6.17647
78 5DXT 5H5 0.04892 0.40272 6.17647
79 4OAS 2SW 0.01232 0.44282 6.25
80 1YP0 PEF 0.03413 0.40296 6.27615
81 4WQ2 3SU 0.04563 0.40692 6.35838
82 2W90 6PG 0.00835 0.42627 6.47059
83 2B96 ANN 0.04037 0.40186 6.50407
84 1E4I NFG 0.02424 0.45377 7.05882
85 4V1T ADP 0.04273 0.40838 7.05882
86 3P9T TCL 0.02265 0.43602 7.30594
87 4OKZ 3E9 0.001273 0.4666 7.35294
88 2Z9I GLY ALA THR VAL 0.03814 0.43317 7.40741
89 5TVI O8N 0.01263 0.45943 7.6087
90 4WT2 3UD 0.01043 0.41453 7.61905
91 2FDW D3G 0.03831 0.427 7.64706
92 5B0I BOG 0.04232 0.4176 7.64706
93 3L9R L9Q 0.001903 0.43346 7.77385
94 4DR9 BB2 0.04408 0.41349 7.8125
95 3GWN FAD 0.03341 0.40839 7.89474
96 1J78 OLA 0.01247 0.46182 7.94118
97 5LX9 OLB 0.01152 0.44436 8.14332
98 1D8C SOR 0.04486 0.43026 8.52941
99 1QY8 RDI 0.03278 0.41724 8.55019
100 5LWY OLB 0.0179 0.43427 8.56164
101 3SP6 IL2 0.03731 0.40866 8.77193
102 1UO5 PIH 0.001816 0.50908 8.82353
103 1UO4 PIH 0.0231 0.43548 8.82353
104 2WH8 II2 0.03008 0.43296 8.82353
105 3G4Q MCH 0.0476 0.41481 8.90411
106 4RC8 STE 0.01952 0.41445 9.00901
107 5KAU RHQ 0.005589 0.44967 9.09091
108 5K53 STE 0.03306 0.40862 9.16031
109 4PPF FLC 0.03793 0.41931 9.41177
110 4LWU 20U 0.04605 0.41248 9.41177
111 1LNX URI 0.01159 0.46288 9.87654
112 1NLI ADE 0.03543 0.40218 10.0806
113 4K7O EKZ 0.03636 0.42443 10.119
114 4YSX E23 0.03071 0.43647 10.5882
115 4DXJ IPE 0.0000001522 0.41368 10.5882
116 4DXJ 0M9 0.0000000877 0.41099 10.5882
117 2P1C GG3 0.000000008361 0.43239 10.8824
118 3EYK EYK 0.003134 0.52934 11.6279
119 4IBF 1D5 0.0276 0.42432 11.6279
120 1DKF OLA 0.03377 0.41966 11.9149
121 5XDT ZI7 0.02086 0.40362 12.013
122 4JZX 476 0.00000004288 0.71922 12.0588
123 4JZB P2H 0.0000002244 0.6999 12.0588
124 4K10 NI9 0.00007445 0.57908 12.0588
125 4JZB IPE 0.002825 0.48086 12.0588
126 4JZX IPE 0.003081 0.47885 12.0588
127 3P5P A3C 0.002212 0.46582 12.6471
128 5CHR 4NC 0.02264 0.4456 13.1387
129 3IX9 MTX 0.02007 0.42514 13.1579
130 4OAR 2S0 0.01417 0.42664 13.1783
131 1OW4 2AN 0.04391 0.42007 13.1783
132 5CUO COA 0.04583 0.40161 13.3663
133 2V5E SCR 0.001412 0.53012 13.8614
134 5TWO 7MV 0.009145 0.4359 13.9706
135 5UNJ RJW 0.02166 0.42659 14.2857
136 4URX FK1 0.01647 0.41678 14.5946
137 2IBZ UQ6 0.04614 0.40146 17.3228
138 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.00602 0.40931 17.3469
139 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.02565 0.44777 17.9916
140 4I67 G G G RPC 0.001795 0.49637 18.3908
141 5OCA 9QZ 0.001446 0.50541 21.4286
142 1YHM AHD 0.0000001188 0.74628 21.4706
143 5DJT FMN 0.03184 0.41211 24.5902
144 1UBY DMA 0.000001272 0.6364 27.9412
145 3LDW ZOL 0.00000007503 0.61981 31.7647
146 3LDW IPE 0.000001542 0.58463 31.7647
147 1K7L 544 0.01575 0.41134 33.3333
148 2HFP NSI 0.02092 0.41053 33.3333
149 3KRO IPE 0.000002067 0.5841 33.5593
150 3KRO DST 0.000002067 0.5841 33.5593
151 3KRO PPV 0.0001143 0.54929 33.5593
152 3WJO IPE 0.0006343 0.52853 35.0148
153 2J1P GRG 0.00002059 0.5538 38.2253
154 4UMJ BFQ 0.0000001021 0.75968 38.5135
155 2O1O RIS 0.00000001126 0.81366 39.1176
156 1RQJ RIS 0.0000002118 0.63407 39.7993
157 1YYE 196 0.02526 0.42636 46.1538
158 3ET3 ET1 0.01304 0.4284 50
159 3ET1 ET1 0.03063 0.41295 50
160 3H0A D30 0.01523 0.40965 50
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