Receptor
PDB id Resolution Class Description Source Keywords
1T0A 1.6 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSP SYNTHASE FROM SHEWANELLA ONEIDENSIS SHEWANELLA ONEIDENSIS MIXED ALPHA BETA HOMOTRIMER SYNTHASE LYASE
Ref.: STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOS SYNTHASE FROM SHEWANELLA ONEIDENSIS AT 1.6 A: IDENT OF FARNESYL PYROPHOSPHATE TRAPPED IN A HYDROPHOBIC ACTA CRYSTALLOGR.,SECT.D V. 60 1949 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:662;
B:761;
C:861;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
58.933 Co [Co+2...
FPP A:1831;
 Valid;
 none;
 submit data
382.326 C15 H28 O7 P2 CC(=C...
ZN A:661;
B:760;
C:860;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1T0A 1.6 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSP SYNTHASE FROM SHEWANELLA ONEIDENSIS SHEWANELLA ONEIDENSIS MIXED ALPHA BETA HOMOTRIMER SYNTHASE LYASE
Ref.: STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOS SYNTHASE FROM SHEWANELLA ONEIDENSIS AT 1.6 A: IDENT OF FARNESYL PYROPHOSPHATE TRAPPED IN A HYDROPHOBIC ACTA CRYSTALLOGR.,SECT.D V. 60 1949 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
3 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
6 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
7 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
8 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
9 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
11 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
12 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
13 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
14 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
15 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
16 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
17 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
18 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
19 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
20 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8I - CIT C6 H8 O7 C(C(=O)O)C....
3 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
6 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
7 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
8 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
9 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
11 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
12 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
13 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
14 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
15 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
16 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
17 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
18 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
19 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
20 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
21 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
22 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
23 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
24 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
25 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
26 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
27 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
28 2UZH - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: FPP; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 VTP 1 0.975
2 GRG 1 1
3 OTP 1 0.975
4 FPP 1 1
5 ZTP 1 0.975
6 GPP 0.911111 0.974359
7 DSL 0.744681 0.9
8 0K3 0.744681 0.9
9 FJP 0.744681 0.923077
10 FDF 0.727273 0.904762
11 FFF 0.714286 0.928571
12 HZZ 0.680851 0.897436
13 FGG 0.590164 0.928571
14 FPF 0.57377 0.928571
15 2CF 0.57377 0.928571
16 ELU 0.571429 0.951219
17 ELR 0.571429 0.951219
18 10E 0.568627 0.702128
19 10D 0.568627 0.785714
20 MGM 0.5625 0.764706
21 DMA 0.5625 0.846154
22 A4S 0.558824 0.698113
23 3E9 0.555556 0.951219
24 FPS 0.551724 0.880952
25 GGS 0.551724 0.880952
26 H6P 0.54902 0.785714
27 FPQ 0.539683 0.826087
28 10G 0.538462 0.767442
29 FII 0.507937 0.666667
30 GST 0.482759 0.857143
31 PS7 0.48 0.906977
32 C0X 0.477612 0.744681
33 FHP 0.473684 0.761905
34 1NH 0.457831 0.770833
35 0FV 0.442623 0.904762
36 LA6 0.442623 0.904762
37 SZH 0.428571 0.655172
38 749 0.428571 0.897436
39 9GB 0.415094 0.825
Similar Ligands (3D)
Ligand no: 1; Ligand: FPP; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1T0A; Ligand: FPP; 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: 1t0a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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