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Receptor
PDB id Resolution Class Description Source Keywords
1Q5H 2 Å EC: 3.-.-.- HUMAN DUTP PYROPHOSPHATASE COMPLEX WITH DUDP HOMO SAPIENS DNA REPAIR ENZYME-DNA INTERACTIONS HYDROLASE
Ref.: HUMAN DUTP PYROPHOSPHATASE: URACIL RECOGNITION BY A HAIRPIN AND ACTIVE SITES FORMED BY THREE SEPARATE S STRUCTURE V. 4 1077 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUD A:779;
B:778;
C:777;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
388.162 C9 H14 N2 O11 P2 C1[C@...
MG A:999;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Q5H 2 Å EC: 3.-.-.- HUMAN DUTP PYROPHOSPHATASE COMPLEX WITH DUDP HOMO SAPIENS DNA REPAIR ENZYME-DNA INTERACTIONS HYDROLASE
Ref.: HUMAN DUTP PYROPHOSPHATASE: URACIL RECOGNITION BY A HAIRPIN AND ACTIVE SITES FORMED BY THREE SEPARATE S STRUCTURE V. 4 1077 1996
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 1Q5H - DUD C9 H14 N2 O11 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 3EHW - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5H4J Ki = 0.13 uM FKM C21 H29 N3 O6 S C[C@H](c1c....
3 2HQU Kd = 1.6 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 3ARA ic50 = 0.32 uM MKH C24 H27 N3 O5 S c1ccc(cc1)....
5 3ARN ic50 = 3.9 uM MSJ C17 H23 N3 O5 S CC(C)(CCCO....
6 1Q5H - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
7 2OKE - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 2OL1 - UMP C9 H13 N2 O8 P 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: DUD; Similar ligands found: 86
No: Ligand ECFP6 Tc MDL keys Tc
1 DUD 1 1
2 DUT 0.880597 1
3 UMP 0.8 0.985075
4 DU 0.8 0.985075
5 DUP 0.739726 0.971014
6 UC5 0.71831 0.985294
7 DUN 0.69863 0.971014
8 DUS 0.642857 0.842105
9 DUR 0.630769 0.867647
10 TYD 0.61039 0.957143
11 YYY 0.589744 0.929577
12 UDP 0.571429 0.913043
13 TTP 0.542169 0.957143
14 UM3 0.540541 0.941176
15 DCP 0.52381 0.929577
16 DU DU DU DU BRU DU DU 0.52 0.853333
17 UTP 0.512195 0.913043
18 DDN 0.506494 0.985075
19 UFP 0.493671 0.916667
20 DDU 0.485714 0.742857
21 8GD 0.477778 0.8375
22 TMP 0.469136 0.942857
23 BRU 0.469136 0.916667
24 5HU 0.469136 0.957143
25 8DD 0.467391 0.844156
26 DU4 0.465909 0.75
27 5IU 0.463415 0.916667
28 UNP 0.45977 0.887324
29 DUA 0.45977 0.797297
30 DU3 0.45977 0.794521
31 6U4 0.457447 0.857143
32 DC 0.451219 0.915493
33 DCM 0.451219 0.915493
34 DAU 0.44898 0.891892
35 TLO 0.442105 0.90411
36 18T 0.438776 0.891892
37 TRH 0.438776 0.891892
38 1JB 0.438776 0.891892
39 U5P 0.4375 0.898551
40 U 0.4375 0.898551
41 UDX 0.4375 0.887324
42 UAD 0.4375 0.887324
43 0FX 0.435644 0.868421
44 BVP 0.431818 0.929577
45 T3Q 0.43 0.868421
46 T3F 0.43 0.868421
47 139 0.428571 0.8125
48 ATY 0.428571 0.90411
49 8DG 0.427083 0.8375
50 T46 0.425743 0.891892
51 UDH 0.425532 0.891892
52 TDX 0.424242 0.90411
53 3R2 0.424242 0.88
54 MMF 0.421569 0.868421
55 GUD 0.421053 0.861111
56 URM 0.421053 0.901408
57 660 0.421053 0.901408
58 UPG 0.421053 0.861111
59 UFM 0.421053 0.861111
60 GDU 0.421053 0.861111
61 2KH 0.420455 0.887324
62 AZD 0.419355 0.868421
63 UPU 0.417582 0.859155
64 3YN 0.415842 0.891892
65 DWN 0.415842 0.868421
66 DGI 0.414894 0.7875
67 UMC 0.414634 0.927536
68 QDM 0.413462 0.857143
69 0N2 0.411765 0.857143
70 UPP 0.410526 0.861111
71 AKM 0.409524 0.848101
72 FNF 0.409524 0.88
73 1YF 0.409524 0.88
74 UFG 0.408163 0.815789
75 PUP 0.408163 0.942029
76 U2F 0.408163 0.815789
77 UPF 0.408163 0.815789
78 UA3 0.407407 0.884058
79 U2P 0.407407 0.898551
80 U3P 0.407407 0.884058
81 UDP UDP 0.406977 0.857143
82 3UC 0.405941 0.815789
83 4TG 0.40566 0.88
84 44P 0.404762 0.928571
85 DUX 0.404494 0.746667
86 PUA 0.4 0.846154
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Q5H; Ligand: DUD; Similar sites found with APoc: 60
This union binding pocket(no: 1) in the query (biounit: 1q5h.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1PTR PRB None
2 1ZEI CRS None
3 5TED SKM None
4 2F6U CIT 2.04082
5 1H3F TYE 2.04082
6 5J60 FAD 2.72109
7 5EOB 5QQ 2.72109
8 1XF1 CIT 2.72109
9 2WD7 VGD 3.40136
10 5AOA PPI 3.40136
11 4JLS 3ZE 4.08163
12 4JD0 1KH 4.08163
13 4DYG MES 4.08163
14 3QVL 5HY 4.08163
15 2F7A CCU 4.08163
16 1OFS SUC 4.08163
17 2F7A BEZ 4.08163
18 4DE3 DN8 4.7619
19 6HKE MLT 4.7619
20 6HKE LMR 4.7619
21 3PE2 E1B 5.44218
22 1J71 THR ILE THR SER 5.44218
23 1ZGS XMM 5.44218
24 2F5Z FAD 5.44218
25 1FL2 FAD 6.12245
26 4RPM HXC 6.12245
27 1O5O U5P 6.12245
28 4UP3 FAD 6.80272
29 5G3U FDA 6.80272
30 2VVL FAD 6.80272
31 5EHS 2JJ 7.48299
32 5EHS 5OY 7.48299
33 2V2V V12 8.16327
34 1TV5 ORO 8.16327
35 4P83 U5P 8.16327
36 1PS9 FAD 8.16327
37 2Q0L FAD 8.84354
38 5M67 NAD 8.84354
39 5M67 3D1 8.84354
40 4B2D SER 9.52381
41 3HRD FAD 9.52381
42 1XS1 DUT 10.2041
43 5EY0 ILE 10.2041
44 5H6S HDH 10.2041
45 1QK3 5GP 10.2041
46 2G50 ALA 10.2041
47 1F76 ORO 10.2041
48 1V59 FAD 10.8844
49 2JB2 FAD 11.5646
50 2JB2 PHE 11.5646
51 5HSA FAS 11.5646
52 3OZG SSI 12.9252
53 2WE0 UMP 14.966
54 5Y6Q FAD 15.6463
55 3FXU TSU 21.0884
56 2J9D ADP 24.3697
57 4XJC TTP 26.5306
58 3T64 DU3 29.932
59 2D4N DUP 43.5374
60 1SJN DUP 49.6599
Pocket No.: 2; Query (leader) PDB : 1Q5H; Ligand: DUD; Similar sites found with APoc: 41
This union binding pocket(no: 2) in the query (biounit: 1q5h.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1BKJ FMN None
2 6EAC ANP 2.72109
3 16PK BIS 3.40136
4 3IQE F42 4.08163
5 1T5B FMN 4.7619
6 1L6O SER LEU LYS LEU MET THR THR VAL 5.26316
7 4IV9 FAD 5.44218
8 1IYE PGU 5.44218
9 1VPE ANP 5.44218
10 1JXZ BCA 6.12245
11 1E8G FAD 6.12245
12 1E8G FCR 6.12245
13 1NZY BCA 6.12245
14 1N07 ADP 6.12245
15 1N07 FMN 6.12245
16 4ITM ATP 6.12245
17 1H74 ADP 6.80272
18 4KQL 1SG 6.80272
19 4XT8 TMQ 6.80272
20 4XT8 NAP 6.80272
21 1UPF URF 7.48299
22 3KLJ FAD 7.48299
23 2ZXI FAD 8.84354
24 1PVC ILE SER GLU VAL 8.84354
25 1VLJ NAP 9.52381
26 3NRZ FAD 9.52381
27 1EK6 UPG 9.52381
28 1EK6 NAI 9.52381
29 3QDL FMN 9.52381
30 2ZJ1 ARJ 10.2041
31 2ZJ1 NAD 10.2041
32 3UN3 G16 10.2041
33 2JLD AG1 11.5646
34 1OFD AKG 12.9252
35 1OFD FMN 12.9252
36 5HJQ I3P 13.6054
37 1KQN NAD 13.6054
38 2Q4W FAD 14.2857
39 4JB1 FAD 17.0068
40 2QXX TTP 23.8095
41 4BQO COA 32.6531
Pocket No.: 3; Query (leader) PDB : 1Q5H; Ligand: DUD; Similar sites found with APoc: 15
This union binding pocket(no: 3) in the query (biounit: 1q5h.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 2ZUX RAM 3.40136
3 1XKQ NDP 4.08163
4 4P87 4NP 4.08163
5 1A0J BEN 4.08163
6 6CAM BGC 4.7619
7 5MRH Q9Z 5.44218
8 3W8X FAD 5.44218
9 3W8X FTK 5.44218
10 2XOC ADE 5.44218
11 5XDT MB3 6.12245
12 3ABI NAD 8.84354
13 2Z49 AMG 9.52381
14 1VBO MAN MAN MAN 11.5646
15 3AB4 THR 12.9252
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