Receptor
PDB id Resolution Class Description Source Keywords
1syl 1.95 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF INACTIVE MUTANT DUTPASE COMPLEXED WITH DUTP ESCHERICHIA COLI ENZYME-LIGAND COMPLEX JELLY ROLL HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF PHOSPHATE ESTER HYDROLYSIS BY DUTPASE J.BIOL.CHEM. V. 279 42907 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUT A:777;
 Valid;
 none;
 submit data
468.142 C9 H15 N2 O14 P3 C1[C@...
MG A:997;
 Invalid;
 none;
 submit data
24.305 Mg [Mg+2...
TRS A:501;
A:502;
 Invalid;
Invalid;
 none;
none;
 submit data
122.143 C4 H12 N O3 C(C(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: DUT; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 DUT 1 1
2 DUD 0.880597 1
3 UMP 0.753623 0.985075
4 DU 0.753623 0.985075
5 DUP 0.701299 0.971014
6 UC5 0.68 0.985294
7 DUN 0.662338 0.971014
8 DUT MG 0.6375 0.941176
9 TTP 0.62963 0.957143
10 DCP 0.609756 0.929577
11 DUS 0.608108 0.842105
12 UMP AF3 PO4 0.60241 0.864865
13 UTP 0.6 0.913043
14 DUR 0.594203 0.867647
15 U5F 0.592593 0.913043
16 F6G 0.564706 0.890411
17 TYD 0.542169 0.957143
18 6U4 0.532609 0.857143
19 UDP 0.52439 0.913043
20 YYY 0.52381 0.929577
21 UM3 0.512821 0.941176
22 8DG 0.5 0.8375
23 DU DU DU DU BRU DU DU 0.485714 0.853333
24 DDN 0.481481 0.985075
25 UFP 0.46988 0.916667
26 DAU 0.46 0.891892
27 DDU 0.459459 0.742857
28 UNP 0.455556 0.887324
29 TLO 0.453608 0.90411
30 1JB 0.45 0.891892
31 18T 0.45 0.891892
32 TRH 0.45 0.891892
33 UAD 0.44898 0.887324
34 UDX 0.44898 0.887324
35 5HU 0.447059 0.957143
36 TMP 0.447059 0.942857
37 BRU 0.447059 0.916667
38 0FX 0.446602 0.868421
39 DU4 0.445652 0.75
40 5IU 0.44186 0.916667
41 T3F 0.441176 0.868421
42 T3Q 0.441176 0.868421
43 DU3 0.43956 0.794521
44 DUA 0.43956 0.797297
45 DGT 0.438776 0.7875
46 139 0.438596 0.8125
47 UDH 0.4375 0.891892
48 T46 0.436893 0.891892
49 TDX 0.435644 0.90411
50 3R2 0.435644 0.88
51 U5P 0.433735 0.898551
52 U 0.433735 0.898551
53 UPG 0.43299 0.861111
54 GDU 0.43299 0.861111
55 UFM 0.43299 0.861111
56 MMF 0.432692 0.868421
57 DCM 0.430233 0.915493
58 DC 0.430233 0.915493
59 3YN 0.427184 0.891892
60 DWN 0.427184 0.868421
61 8GD 0.427083 0.8375
62 QDM 0.424528 0.857143
63 BUP 0.423913 0.851351
64 0N2 0.423077 0.857143
65 UPP 0.42268 0.861111
66 523 0.421053 0.881579
67 AKM 0.420561 0.848101
68 FNF 0.420561 0.88
69 1YF 0.420561 0.88
70 UFG 0.42 0.815789
71 U2F 0.42 0.815789
72 UPF 0.42 0.815789
73 8DD 0.418367 0.844156
74 URM 0.418367 0.901408
75 660 0.418367 0.901408
76 2KH 0.417582 0.887324
77 3UC 0.417476 0.815789
78 4TG 0.416667 0.88
79 0KX 0.414894 0.90411
80 UPU 0.414894 0.859155
81 AWU 0.414141 0.861111
82 D3T 0.413043 0.929577
83 BVP 0.413043 0.929577
84 PUA 0.409836 0.846154
85 G3N 0.407767 0.888889
86 JHZ 0.407407 0.846154
87 44P 0.402299 0.928571
88 T5A 0.401709 0.804878
Similar Ligands (3D)
Ligand no: 1; Ligand: DUT; Similar ligands found: 21
No: Ligand Similarity coefficient
1 MG TTP 0.9799
2 DTP 0.9505
3 HF4 0.9484
4 DZ4 0.9437
5 HF7 0.9182
6 HEJ 0.9078
7 CTP 0.9057
8 HDV 0.9022
9 2TM 0.8920
10 GTF 0.8904
11 FZQ 0.8882
12 DCT 0.8862
13 ANP 0.8825
14 FZK 0.8822
15 7D4 0.8807
16 ATP 0.8788
17 HFD 0.8634
18 CDP 0.8631
19 3AT 0.8618
20 FZT 0.8615
21 ACP 0.8592
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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