Receptor
PDB id Resolution Class Description Source Keywords
5GP0 1.7 Å EC: 3.6.1.55 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
6FL4 1.6 Å EC: 3.6.1.55 A. THALIANA NUDT1 IN COMPLEX WITH 8-OXO-DGTP ARABIDOPSIS THALIANA 8-OXO-DGTP HYDROLASE
Ref.: CRYSTAL STRUCTURE AND SUBSTRATE SPECIFICITY OF THE 8-OXO-DGTP HYDROLASE NUDT1 FROM ARABIDOPSIS THALIAN BIOCHEMISTRY V. 58 887 2019
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6FL4 - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
2 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
3 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6FL4 - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
2 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
3 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
4 6YPF - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6FL4 - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
2 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
3 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
4 6YPF - GPP C10 H20 O7 P2 CC(=CCC/C(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GPP; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 ZTP 0.911111 0.95
3 GRG 0.911111 0.974359
4 VTP 0.911111 0.95
5 OTP 0.911111 0.95
6 FPP 0.911111 0.974359
7 HZZ 0.704545 0.921053
8 FFF 0.672727 0.904762
9 FJP 0.659574 0.897436
10 0K3 0.659574 0.875
11 DSL 0.659574 0.875
12 FDF 0.654545 0.880952
13 10E 0.617021 0.717391
14 10D 0.617021 0.804878
15 DMA 0.613636 0.868421
16 H6P 0.595745 0.804878
17 10G 0.583333 0.785714
18 A4S 0.545455 0.711538
19 FPF 0.533333 0.904762
20 2CF 0.533333 0.904762
21 FGG 0.52459 0.904762
22 GST 0.518519 0.878049
23 3E9 0.516129 0.926829
24 ELU 0.507937 0.926829
25 ELR 0.507937 0.926829
26 MGM 0.5 0.745098
27 FPS 0.482759 0.857143
28 GGS 0.482759 0.857143
29 FPQ 0.47619 0.804348
30 0FV 0.473684 0.926829
31 LA6 0.473684 0.926829
32 749 0.461538 0.871795
33 1NH 0.444444 0.787234
34 FII 0.444444 0.649123
35 SZH 0.432432 0.637931
36 PS7 0.426667 0.883721
37 9GB 0.42 0.846154
38 C0X 0.41791 0.723404
39 FHP 0.403509 0.738095
40 9AX 0.4 0.826087
Similar Ligands (3D)
Ligand no: 1; Ligand: GPP; Similar ligands found: 2
No: Ligand Similarity coefficient
1 RZ5 0.8765
2 86B 0.8716
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6FL4; Ligand: 8DG; 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: 6fl4.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6FL4; Ligand: 8DG; 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: 6fl4.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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