Receptor
PDB id Resolution Class Description Source Keywords
5GP0 1.7 Å EC: 3.6.1.55_3.6.1.67_3.6.1.22 CRYSTAL STRUCTURE OF GERANIOL-NUDX1 COMPLEX ARABIDOPSIS THALIANA GERANIOL NUDX1 ARABIDOPSIS THALIANA COMPLEX HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE SUBSTRATE RECOGNITION OF ARABIDOPSIS GPP-BOUND NUDX1 FOR NONCANONICAL MON BIOSYNTHESIS. MOL PLANT V. 11 218 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL E:201;
I:201;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
GPP F:201;
A:201;
E:202;
I:202;
Valid;
Valid;
Valid;
Valid;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
submit data
314.209 C10 H20 O7 P2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GP0 1.7 Å EC: 3.6.1.55_3.6.1.67_3.6.1.22 CRYSTAL STRUCTURE OF GERANIOL-NUDX1 COMPLEX ARABIDOPSIS THALIANA GERANIOL NUDX1 ARABIDOPSIS THALIANA COMPLEX HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE SUBSTRATE RECOGNITION OF ARABIDOPSIS GPP-BOUND NUDX1 FOR NONCANONICAL MON BIOSYNTHESIS. MOL PLANT V. 11 218 2018
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GPP; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 OTP 0.911111 0.95
3 FPP 0.911111 0.974359
4 VTP 0.911111 0.95
5 ZTP 0.911111 0.95
6 GRG 0.911111 0.974359
7 FFF 0.672727 0.904762
8 DSL 0.659574 0.875
9 0K3 0.659574 0.875
10 FJP 0.659574 0.897436
11 FDF 0.654545 0.880952
12 10E 0.617021 0.717391
13 10D 0.617021 0.804878
14 DMA 0.613636 0.868421
15 H6P 0.595745 0.804878
16 10G 0.583333 0.785714
17 A4S 0.545455 0.711538
18 FPF 0.533333 0.904762
19 2CF 0.533333 0.904762
20 FGG 0.52459 0.904762
21 GST 0.518519 0.878049
22 3E9 0.516129 0.926829
23 MGM 0.5 0.745098
24 FPS 0.482759 0.857143
25 GGS 0.482759 0.857143
26 FPQ 0.47619 0.804348
27 LA6 0.473684 0.926829
28 0FV 0.473684 0.926829
29 749 0.461538 0.871795
30 1NH 0.444444 0.787234
31 FII 0.444444 0.649123
32 SZH 0.432432 0.637931
33 PS7 0.426667 0.883721
34 9GB 0.42 0.846154
35 FHP 0.403509 0.738095
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GP0; Ligand: GPP; 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: 5gp0.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5gp0.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5gp0.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5gp0.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5gp0.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5gp0.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5gp0.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5gp0.bio3) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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