Receptor
PDB id Resolution Class Description Source Keywords
2E8U 2.08 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM AND IPP (P21) SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE FARNESYL PYROPHOSPHATE BISPHOSPHONATE
Ref.: BISPHOSPHONATES TARGET MULTIPLE SITES IN BOTH CIS-AND TRANS-PRENYLTRANSFERASES PROC.NATL.ACAD.SCI.USA V. 104 10022 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IPE A:1101;
A:1102;
B:1103;
B:1104;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
246.092 C5 H12 O7 P2 CC(=C...
MG A:1301;
A:1302;
B:1303;
B:1304;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 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
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 = 11.22 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 = 11.22 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 (22)
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 = 11.22 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....
22 6R4V Kd = 1.74 uM BFQ C9 H23 N O7 P2 CCCCC[N@](....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: IPE; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 IPE 1 1
2 IP8 0.617647 0.918919
3 0O3 0.589744 0.871795
4 0CJ 0.536585 0.780488
5 P23 0.527778 0.815789
6 ISY 0.487805 0.85
7 DED 0.487179 0.653061
8 IPR 0.475 0.820513
9 P25 0.463415 0.825
10 P22 0.444444 0.710526
11 43W 0.439024 0.789474
12 0CH 0.439024 0.731707
13 EIP 0.431818 0.846154
14 DMA 0.428571 0.794872
15 0JX 0.428571 0.810811
16 0K2 0.418605 0.74359
17 BHI 0.413043 0.767442
18 DP6 0.408163 0.785714
Similar Ligands (3D)
Ligand no: 1; Ligand: IPE; Similar ligands found: 140
No: Ligand Similarity coefficient
1 IS3 0.9735
2 10D 0.9529
3 10E 0.9483
4 H6P 0.9440
5 10G 0.9433
6 DST 0.9412
7 0CN 0.9411
8 2JA 0.9339
9 0CM 0.9331
10 43Q 0.9304
11 RGP 0.9261
12 P3S 0.9259
13 2E5 0.9200
14 2E4 0.9161
15 AZM 0.9151
16 2E6 0.9145
17 PMV 0.9124
18 DLT 0.9121
19 HPO 0.9081
20 0CG 0.9079
21 BGT 0.9058
22 6FR 0.9052
23 I58 0.9029
24 AGP 0.9018
25 G6Q 0.9009
26 MGB 0.9008
27 G88 0.9005
28 3PO 0.8983
29 DG2 0.8982
30 ATX 0.8980
31 PA5 0.8962
32 M3L 0.8957
33 58X 0.8948
34 5DS 0.8936
35 ZZU 0.8923
36 DI9 0.8915
37 STX 0.8907
38 CXA 0.8892
39 HSA 0.8888
40 DX5 0.8882
41 5SP 0.8881
42 TX4 0.8878
43 5TO 0.8855
44 NLQ 0.8854
45 88L 0.8850
46 PAN 0.8834
47 NFZ 0.8833
48 CIR 0.8833
49 PPK 0.8830
50 5RP 0.8824
51 ARG 0.8824
52 4TP 0.8823
53 ALA GLU 0.8820
54 0F3 0.8819
55 3CX 0.8813
56 GGB 0.8813
57 RES 0.8811
58 ILO 0.8811
59 GGG 0.8808
60 4NP 0.8793
61 2OR 0.8792
62 EGV 0.8790
63 PNP 0.8789
64 PAU 0.8787
65 DAR 0.8787
66 3UF 0.8784
67 NBB 0.8784
68 AHL 0.8776
69 4MB 0.8774
70 R52 0.8774
71 R5P 0.8774
72 CU0 0.8771
73 NLG 0.8757
74 M3C 0.8756
75 3W3 0.8755
76 A5P 0.8753
77 PTB 0.8753
78 GVA 0.8752
79 2J3 0.8749
80 HCT 0.8743
81 5LD 0.8743
82 GRQ 0.8736
83 64Z 0.8733
84 4NS 0.8732
85 HRG 0.8732
86 D5X 0.8731
87 VFG 0.8731
88 3EB 0.8730
89 DXP 0.8730
90 HAR 0.8728
91 HCA 0.8727
92 HLP 0.8723
93 6C5 0.8713
94 MZM 0.8712
95 ASF 0.8709
96 S6P 0.8702
97 DEZ 0.8697
98 6FG 0.8697
99 5OY 0.8693
100 CPM 0.8692
101 PML 0.8691
102 WT2 0.8690
103 1OS 0.8687
104 M28 0.8684
105 B15 0.8675
106 XOG 0.8672
107 KAP 0.8669
108 FSA 0.8669
109 6C8 0.8668
110 2O8 0.8666
111 U4G 0.8663
112 1PS 0.8661
113 5PV 0.8659
114 HJ7 0.8649
115 1FD 0.8647
116 GG8 0.8647
117 LGT 0.8646
118 GAE 0.8643
119 AES 0.8640
120 E79 0.8640
121 IOP 0.8638
122 API 0.8637
123 VUR 0.8637
124 6PG 0.8634
125 3XR 0.8622
126 DER 0.8612
127 U7E 0.8609
128 FM4 0.8605
129 4JE 0.8599
130 23N 0.8596
131 BSC 0.8587
132 GLY GLY GLY 0.8579
133 ING 0.8576
134 2JJ 0.8569
135 EUE 0.8565
136 0QA 0.8564
137 K4V 0.8541
138 LRW 0.8540
139 CS2 0.8539
140 KDG 0.8525
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Z7I; Ligand: 742; 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: 2z7i.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2Z7I; Ligand: 742; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 2z7i.bio1) has 65 residues
No: Leader PDB Ligand Sequence Similarity
1 4DXJ 0M9 10.5882
2 1YHM AHD 21.4706
3 1YHM AHD 21.4706
4 1YHM AHD 21.4706
5 3LDW ZOL 31.7647
6 4UMJ BFQ 38.5135
7 4UMJ BFQ 38.5135
8 2O1O RIS 39.1176
9 2O1O RIS 39.1176
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