Receptor
PDB id Resolution Class Description Source Keywords
6HDE 1.82 Å EC: 3.6.1.23 STRUCTURE OF ESCHERICHIA COLI DUTPASE Q93H MUTANT ESCHERICHIA COLI (STRAIN K12) DUTPASE HOMOTRIMER MUTANT HYDROLASE
Ref.: THE ROLE OF A KEY AMINO ACID POSITION IN SPECIES-SP PROTEINACEOUS DUTPASE INHIBITION. BIOMOLECULES V. 9 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:203;
C:201;
B:202;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
DUP A:202;
B:201;
A:201;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 60.8 nM
467.157 C9 H16 N3 O13 P3 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6HDE 1.82 Å EC: 3.6.1.23 STRUCTURE OF ESCHERICHIA COLI DUTPASE Q93H MUTANT ESCHERICHIA COLI (STRAIN K12) DUTPASE HOMOTRIMER MUTANT HYDROLASE
Ref.: THE ROLE OF A KEY AMINO ACID POSITION IN SPECIES-SP PROTEINACEOUS DUTPASE INHIBITION. BIOMOLECULES V. 9 2019
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
3 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
4 6HDE Kd = 60.8 nM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
8 2HRM Kd = 278.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
3 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
4 6HDE Kd = 60.8 nM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
8 2HRM Kd = 278.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1SJN - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
4 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
5 6HDE Kd = 60.8 nM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
9 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
10 1SNF - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DUP; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 DU 0.742857 0.956522
4 UMP 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUT MG 0.62963 0.914286
9 0KX 0.614458 0.931507
10 DUS 0.6 0.820513
11 UMP AF3 PO4 0.595238 0.842105
12 DUR 0.585714 0.842857
13 2KH 0.585366 0.915493
14 UM3 0.506329 0.914286
15 DU DU DU DU BRU DU DU 0.495238 0.831169
16 DDN 0.47561 0.956522
17 DU4 0.472527 0.730769
18 BRU 0.458824 0.891892
19 DDU 0.453333 0.722222
20 DU3 0.450549 0.773333
21 DUA 0.450549 0.776316
22 TYD 0.449438 0.930556
23 UFP 0.447059 0.891892
24 TMP 0.44186 0.916667
25 5HU 0.44186 0.930556
26 5IU 0.436782 0.891892
27 UNP 0.434783 0.915493
28 YYY 0.433333 0.90411
29 UDP 0.431818 0.887324
30 TTP 0.430108 0.930556
31 DCM 0.425287 0.890411
32 DC 0.425287 0.890411
33 UTP 0.417582 0.887324
34 DCP 0.414894 0.90411
35 U5F 0.413043 0.887324
36 U 0.411765 0.873239
37 U5P 0.411765 0.873239
38 BVP 0.408602 0.90411
39 DZ4 0.40404 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: DUP; Similar ligands found: 14
No: Ligand Similarity coefficient
1 MG TTP 0.9430
2 ANP 0.9039
3 7D4 0.8940
4 FZQ 0.8841
5 2TM 0.8798
6 CTP 0.8797
7 ATP 0.8755
8 FZK 0.8750
9 3AT 0.8719
10 HF4 0.8636
11 AHX 0.8630
12 AGS 0.8579
13 ACP 0.8558
14 8DG 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6HDE; Ligand: DUP; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 6hde.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6KZ6 UMP 32.2581
2 6KZ6 UMP 32.2581
3 6KZ6 UMP 32.2581
Pocket No.: 2; Query (leader) PDB : 6HDE; Ligand: DUP; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 6hde.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 6KZ6 UMP 32.2581
2 6KZ6 UMP 32.2581
3 5Y5Q DUT 35.5263
4 5Y5Q DUT 35.5263
5 6KY9 UMP 39.4737
6 6KY9 UMP 39.4737
7 6KY9 UMP 39.4737
Pocket No.: 3; Query (leader) PDB : 6HDE; Ligand: DUP; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 6hde.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6KZ6 UMP 32.2581
2 6KZ6 UMP 32.2581
APoc FAQ
Feedback