Receptor
PDB id Resolution Class Description Source Keywords
2HRM 1.7 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOG METHYLENE-DUTP ESCHERICHIA COLI JELLY ROLL ENZYME-SUBSTRATE ANALOGUE LIGAND COMPLEX HYDROL
Ref.: METHYLENE SUBSTITUTION AT THE ALPHA-BETA BRIDGING P WITHIN THE PHOSPHATE CHAIN OF DUDP PROFOUNDLY PERTU LIGAND ACCOMMODATION INTO THE DUTPASE ACTIVE SITE. PROTEINS V. 71 308 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:301;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
UC5 A:777;
Valid;
none;
Kd = 287.5 uM
386.189 C10 H16 N2 O10 P2 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 = 287.5 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 = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 5NYZ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5CCO - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5CCT - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 4GV8 Kd = 0.32 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 3EHW - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 5H4J Ki = 0.13 uM FKM C21 H29 N3 O6 S C[C@H](c1c....
7 2HQU Kd = 1.6 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 3ARA ic50 = 0.32 uM MKH C24 H27 N3 O5 S c1ccc(cc1)....
9 3ARN ic50 = 3.9 uM MSJ C17 H23 N3 O5 S CC(C)(CCCO....
10 3P48 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
11 1Q5H - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
12 4OOP - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
13 1F7N - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1F7Q - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
15 1F7P - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
16 3F4F - UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1DUC - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
18 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
19 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
20 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
21 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
22 2OL0 - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
23 2OKE - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
24 2OL1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
25 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
26 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UC5; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 UC5 1 1
2 DU 0.772727 0.970588
3 UMP 0.772727 0.970588
4 DUD 0.71831 0.985294
5 DUN 0.69863 0.957143
6 DUT 0.68 0.985294
7 DUP 0.671053 0.957143
8 DUS 0.642857 0.831169
9 DUR 0.606061 0.855072
10 44P 0.573333 0.942857
11 UM3 0.52 0.927536
12 DDN 0.506494 0.970588
13 DU DU DU DU BRU DU DU 0.490196 0.842105
14 DDU 0.485714 0.732394
15 DUA 0.45977 0.786667
16 DU3 0.45977 0.783784
17 UFP 0.45679 0.90411
18 U 0.455696 0.885714
19 U5P 0.455696 0.885714
20 TMP 0.451219 0.929577
21 5HU 0.451219 0.943662
22 BRU 0.451219 0.90411
23 DU4 0.449438 0.74026
24 5IU 0.445783 0.90411
25 UDP 0.440476 0.9
26 DCM 0.433735 0.902778
27 DC 0.433735 0.902778
28 TYD 0.425287 0.943662
29 UTP 0.425287 0.9
30 U5F 0.420455 0.9
31 Y6W 0.416667 0.878378
32 BVP 0.41573 0.916667
33 UNP 0.411111 0.875
34 YYY 0.409091 0.916667
35 UDX 0.408163 0.875
36 UAD 0.408163 0.875
37 UDP UDP 0.406977 0.84507
38 TTP 0.406593 0.943662
39 2KH 0.404494 0.875
40 UPU 0.402174 0.847222
41 TTP MG 0.402174 0.888889
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
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