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
1RN8 1.93 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE IMIDO-DUTP ESCHERICHIA COLI JELLY ROLL ENZYME-LIGAND COMPLEX HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF PHOSPHATE ESTER HYDROLYSIS BY DUTPASE. J.BIOL.CHEM. V. 279 42907 2004
Members (7)
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 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
7 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
70% Homology Family (7)
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 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
7 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 204 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: 39
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 DU3 0.45977 0.783784
16 DUA 0.45977 0.786667
17 UFP 0.45679 0.90411
18 U 0.455696 0.885714
19 U5P 0.455696 0.885714
20 5HU 0.451219 0.943662
21 BRU 0.451219 0.90411
22 TMP 0.451219 0.929577
23 DU4 0.449438 0.74026
24 5IU 0.445783 0.90411
25 UDP 0.440476 0.9
26 DC 0.433735 0.902778
27 DCM 0.433735 0.902778
28 UTP 0.425287 0.9
29 TYD 0.425287 0.943662
30 Y6W 0.416667 0.878378
31 BVP 0.41573 0.916667
32 UNP 0.411111 0.875
33 YYY 0.409091 0.916667
34 UAD 0.408163 0.875
35 UDX 0.408163 0.875
36 UDP UDP 0.406977 0.84507
37 TTP 0.406593 0.943662
38 2KH 0.404494 0.875
39 UPU 0.402174 0.847222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RN8; Ligand: DUP; 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: 1rn8.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1RN8; Ligand: DUP; 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: 1rn8.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1RN8; Ligand: DUP; 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: 1rn8.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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