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Receptor
PDB id Resolution Class Description Source Keywords
3P48 1.67 Å EC: 3.6.1.23 STRUCTURE OF THE YEAST DUTPASE DUT1 IN COMPLEX WITH DUMPNPP SACCHAROMYCES CEREVISIAE TRIMER BETA BARREL DUMPPNP PYROPHOSPHATASE HYDROLASE PHOSPHOPROTEIN STRUCTURAL GENOMICS ONTARIO CENTRE FOR STRPROTEOMICS OCSP
Ref.: STRUCTURE AND ACTIVITY OF THE SACCHAROMYCES CEREVIS PYROPHOSPHATASE DUT1, AN ESSENTIAL HOUSEKEEPING ENZ BIOCHEM.J. V. 437 243 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUP B:149;
A:148;
B:148;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
467.157 C9 H16 N3 O13 P3 C1[C@...
MG C:148;
A:149;
B:150;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3P48 1.67 Å EC: 3.6.1.23 STRUCTURE OF THE YEAST DUTPASE DUT1 IN COMPLEX WITH DUMPNPP SACCHAROMYCES CEREVISIAE TRIMER BETA BARREL DUMPPNP PYROPHOSPHATASE HYDROLASE PHOSPHOPROTEIN STRUCTURAL GENOMICS ONTARIO CENTRE FOR STRPROTEOMICS OCSP
Ref.: STRUCTURE AND ACTIVITY OF THE SACCHAROMYCES CEREVIS PYROPHOSPHATASE DUT1, AN ESSENTIAL HOUSEKEEPING ENZ BIOCHEM.J. V. 437 243 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3P48 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 3P48 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 3F4F - 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: DUP; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 UMP 0.742857 0.956522
4 DU 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUS 0.6 0.820513
9 DUR 0.585714 0.842857
10 2KH 0.585366 0.915493
11 UM3 0.506329 0.914286
12 DU DU DU DU BRU DU DU 0.495238 0.831169
13 DDN 0.47561 0.956522
14 DU4 0.472527 0.730769
15 BRU 0.458824 0.891892
16 DDU 0.453333 0.722222
17 DUA 0.450549 0.776316
18 DU3 0.450549 0.773333
19 TYD 0.449438 0.930556
20 UFP 0.447059 0.891892
21 TMP 0.44186 0.916667
22 5HU 0.44186 0.930556
23 5IU 0.436782 0.891892
24 UNP 0.434783 0.915493
25 YYY 0.433333 0.90411
26 UDP 0.431818 0.887324
27 TTP 0.430108 0.930556
28 DC 0.425287 0.890411
29 DCM 0.425287 0.890411
30 UTP 0.417582 0.887324
31 DCP 0.414894 0.90411
32 U 0.411765 0.873239
33 U5P 0.411765 0.873239
34 BVP 0.408602 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3P48; Ligand: DUP; Similar sites found with APoc: 75
This union binding pocket(no: 1) in the query (biounit: 3p48.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3FW3 GLC None
2 1ZEI CRS None
3 5NTW 98N None
4 4FGC PQ0 1.36054
5 4CS9 AMP 2.04082
6 1L1Q 9DA 2.04082
7 6GN6 MAL 2.72109
8 2OFE NAG 2.8169
9 4EDF UPG 3.40136
10 4B2D SER 3.40136
11 3QDL FMN 3.40136
12 1HZP DAO 3.40136
13 6DWD HDV 4.08163
14 6DWD GTP 4.08163
15 5TS5 FAD 4.08163
16 4JB1 FAD 4.41176
17 4JB1 NAP 4.41176
18 2FXV 5GP 4.7619
19 5M67 ADE 4.7619
20 4P83 U5P 4.7619
21 5M67 NAD 4.7619
22 5M67 3D1 4.7619
23 2V2V V12 4.7619
24 3E3U NVC 4.7619
25 1T3Q FAD 5.44218
26 1T3Q MCN 5.44218
27 4ITM ATP 5.44218
28 1PZM 5GP 5.44218
29 1JXZ BCA 6.12245
30 1NZY BCA 6.12245
31 5HP8 PYR 6.45161
32 1Q19 APC 6.80272
33 3QDY CBS 6.99301
34 4Z2S NDG 7.04225
35 4Z2S NAG 7.04225
36 1DKU AP2 7.48299
37 4P86 5GP 7.48299
38 3OND ADN 8.16327
39 3OND NAD 8.16327
40 2AJH MET 8.16327
41 2JBH 5GP 8.16327
42 5HJQ I3P 9.52381
43 5NC9 8SZ 9.52381
44 2UUU FAD 10.2041
45 2UUU PL3 10.2041
46 1N62 FAD 10.2041
47 3NRZ FAD 10.2041
48 2WOX NDP 10.2041
49 2WME NAP 10.2041
50 5Y6Q FAD 10.8844
51 1RC0 KT5 10.8844
52 5N1P 8GK 11.5646
53 3W8X FTK 12.2449
54 3W8X FAD 12.2449
55 4JLS 3ZE 12.2449
56 1BZY IMU 12.2449
57 1XS1 DUT 12.9252
58 5G5G FAD 13.6054
59 5G5G MCN 13.6054
60 1H6H PIB 13.986
61 3HRD FAD 14.2857
62 4Y4V DAL 14.2857
63 1OFD FMN 14.966
64 1OFD AKG 14.966
65 1L6O SER LEU LYS LEU MET THR THR VAL 15.7895
66 5JBE GLC GLC GLC GLC GLC 16.3265
67 3JZ4 NAP 18.3673
68 3FXU TSU 19.0476
69 4XJC TTP 19.7279
70 3BP1 GUN 19.7279
71 1FFU FAD 19.7279
72 4C2C ALA ALA ALA 19.7279
73 3W6G FLC 21.0884
74 2QXX TTP 25.1701
75 3OZG SSI 29.932
Pocket No.: 2; Query (leader) PDB : 3P48; Ligand: DUP; Similar sites found with APoc: 25
This union binding pocket(no: 2) in the query (biounit: 3p48.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4B5W PYR None
2 2V5K OXM None
3 4YEF 4CQ 3.37079
4 6EAC ANP 3.40136
5 2HQM FAD 3.40136
6 5J60 FAD 4.08163
7 2DT5 NAD 4.08163
8 5GVR LMR 4.08163
9 2JB2 PHE 4.08163
10 2JB2 FAD 4.08163
11 2VWT PYR 4.7619
12 4XT8 TMQ 6.12245
13 1RL4 BRR 6.12245
14 1HSK FAD 6.80272
15 6D6L FY4 6.80272
16 1UYY BGC BGC 6.87023
17 1YQC GLV 7.48299
18 3W9Z FMN 10.8844
19 3GDN FAD 11.5646
20 5JBX MLI 12.9252
21 1KQN NAD 13.6054
22 1RM6 FAD 17.6871
23 1RM6 PCD 17.6871
24 3RNM FAD 24.1379
25 3V2U ATP 27.8912
Pocket No.: 3; Query (leader) PDB : 3P48; Ligand: DUP; Similar sites found with APoc: 27
This union binding pocket(no: 3) in the query (biounit: 3p48.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5IXB LGA None
2 1QB7 ADE 2.04082
3 2ZJ1 ARJ 2.72109
4 2ZJ1 NAD 2.72109
5 1MZV AMP 2.72109
6 5EB4 FAD 2.72109
7 1E8G FAD 3.40136
8 1E8G FCR 3.40136
9 2BL9 NDP 4.7619
10 2BL9 CP6 4.7619
11 4QIJ 1HA 4.7619
12 4RGQ 13P 5.44218
13 1A8R GTP 5.44218
14 4O33 3PG 6.12245
15 4O33 TZN 6.12245
16 4I4Z 2NE 6.80272
17 3QDV NDG 6.99301
18 3QDW NDG 6.99301
19 3QDU CBS CBS 6.99301
20 3QDX CBS 6.99301
21 3LOO B4P 8.16327
22 4I42 1HA 8.84354
23 6F5W KG1 8.84354
24 5WS9 AMP 10.2041
25 1PVC ILE SER GLU VAL 14.7059
26 4KQL 1SG 14.966
27 1T5B FMN 14.966
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