Receptor
PDB id Resolution Class Description Source Keywords
6DBZ 1.9 Å EC: 3.6.1.55 CRYSTAL STRUCTURE OF NUDIX 1 FROM ARABIDOPSIS THALIANA COMPL ISOPENTENYL DIPHOSPHATE ARABIDOPSIS THALIANA PHOSPHATASE HYDROLASE
Ref.: CONTRIBUTION OF ISOPENTENYL PHOSPHATE TO PLANT TERP METABOLISM. NAT PLANTS V. 4 721 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:202;
B:203;
A:202;
A:204;
B:204;
A:205;
A:203;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
IPR B:201;
A:201;
 Valid;
Valid;
 none;
none;
 submit data
248.108 C5 H14 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: IPR; Similar ligands found: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 IPR 1 1
2 IS3 0.666667 0.918919
3 EIP 0.631579 0.864865
4 P23 0.542857 0.885714
5 DED 0.5 0.772727
6 IPE 0.475 0.820513
7 P25 0.475 0.842105
8 P22 0.457143 0.771429
9 BHI 0.454545 0.780488
10 43W 0.45 0.805556
11 0CH 0.45 0.74359
12 0CJ 0.44186 0.842105
13 0JX 0.439024 0.828571
14 0K2 0.428571 0.805556
15 0O3 0.418605 0.707317
16 DP6 0.416667 0.8
17 0CM 0.414634 0.777778
18 3E9 0.413793 0.829268
19 ELR 0.40678 0.829268
20 ELU 0.40678 0.829268
Similar Ligands (3D)
Ligand no: 1; Ligand: IPR; Similar ligands found: 81
No: Ligand Similarity coefficient
1 DMA 0.9903
2 H6P 0.9393
3 P3S 0.9335
4 2JA 0.9299
5 ISY 0.9280
6 DST 0.9256
7 PMV 0.9213
8 DG2 0.9116
9 58X 0.9112
10 DLT 0.9111
11 43Q 0.9098
12 AZM 0.9037
13 0CG 0.9003
14 6FR 0.8989
15 DX5 0.8986
16 HPO 0.8909
17 G01 0.8893
18 G6Q 0.8886
19 5SP 0.8875
20 ATX 0.8863
21 MGB 0.8859
22 STX 0.8852
23 2E5 0.8850
24 VFG 0.8846
25 AGP 0.8836
26 M3L 0.8819
27 NFZ 0.8815
28 G88 0.8811
29 DI9 0.8792
30 NBB 0.8786
31 ZZU 0.8783
32 A5P 0.8781
33 M3C 0.8765
34 GRQ 0.8762
35 PAU 0.8752
36 LXP 0.8742
37 5TO 0.8728
38 BGT 0.8710
39 2J3 0.8708
40 PML 0.8705
41 DXP 0.8696
42 AHL 0.8687
43 6C9 0.8684
44 ARG 0.8681
45 GVA 0.8679
46 ILO 0.8678
47 PA5 0.8672
48 DAR 0.8672
49 ALA GLU 0.8670
50 HSA 0.8667
51 PTB 0.8654
52 LGT 0.8650
53 GGB 0.8648
54 HAR 0.8647
55 R5P 0.8646
56 GGG 0.8645
57 EXY 0.8639
58 CXA 0.8638
59 VFM 0.8638
60 I58 0.8635
61 S6P 0.8633
62 3CX 0.8633
63 FM4 0.8630
64 MZM 0.8630
65 IOP 0.8629
66 F6R 0.8624
67 TX4 0.8617
68 PAN 0.8599
69 ING 0.8595
70 D1G 0.8592
71 WT2 0.8580
72 2OR 0.8578
73 HLP 0.8577
74 6C5 0.8568
75 CIR 0.8567
76 3PO 0.8565
77 XOG 0.8563
78 M6R 0.8545
79 5PV 0.8535
80 3W6 0.8515
81 FSA 0.8510
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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