Receptor
PDB id Resolution Class Description Source Keywords
2D3Y 1.55 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM THERMUS THE HB8 THERMUS THERMOPHILUS BASE EXCISION REPAIR URACIL-DNA GLYCOSYLASE IRON/SULFER CLTHERMOPHILE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAGENOMICS/PROTEOMICS INITIATIVE RSGI HYDROLASE
Ref.: CRYSTAL STRUCTURE OF FAMILY 5 URACIL-DNA GLYCOSYLAS TO DNA. J.MOL.BIOL. V. 373 839 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:222;
A:223;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
DU A:221;
Valid;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
SF4 A:220;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D3Y 1.55 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM THERMUS THE HB8 THERMUS THERMOPHILUS BASE EXCISION REPAIR URACIL-DNA GLYCOSYLASE IRON/SULFER CLTHERMOPHILE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAGENOMICS/PROTEOMICS INITIATIVE RSGI HYDROLASE
Ref.: CRYSTAL STRUCTURE OF FAMILY 5 URACIL-DNA GLYCOSYLAS TO DNA. J.MOL.BIOL. V. 373 839 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DU; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 UMP 1 1
2 DU 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUT MG 0.684932 0.914286
10 DUR 0.683333 0.852941
11 UMP AF3 PO4 0.675676 0.876712
12 DDN 0.632353 1
13 UFP 0.591549 0.929577
14 BRU 0.583333 0.929577
15 5HU 0.583333 0.942857
16 TMP 0.583333 0.956522
17 UM3 0.57971 0.955224
18 5IU 0.575342 0.929577
19 DCM 0.561644 0.928571
20 DC 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U5P 0.527778 0.911765
24 DDU 0.523077 0.753623
25 UMC 0.520548 0.941176
26 QBT 0.493333 0.927536
27 DUA 0.487805 0.783784
28 DU3 0.487805 0.780822
29 DU4 0.47619 0.76
30 TYD 0.469136 0.942857
31 YYY 0.451219 0.915493
32 UDP 0.45 0.898551
33 TTP 0.447059 0.942857
34 8OG 0.435294 0.835443
35 UA3 0.434211 0.897059
36 U3P 0.434211 0.897059
37 U2P 0.434211 0.884058
38 UTP 0.433735 0.898551
39 44P 0.43038 0.914286
40 DCP 0.430233 0.915493
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 139 0.409091 0.8
45 UPU 0.409091 0.871429
46 U 0.408451 0.771429
47 URI 0.408451 0.771429
48 TBD 0.406977 0.90411
49 PUA 0.405172 0.833333
50 UNP 0.402299 0.873239
51 UDX 0.4 0.873239
52 UAD 0.4 0.873239
53 PUP 0.4 0.955882
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D3Y; Ligand: DU; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 2d3y.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5O4J PJL 0.03582 0.4177 1.82648
2 5O4J SAH 0.0381 0.41631 1.82648
3 5O4J 9KH 0.0381 0.41631 1.82648
4 1RO7 CSF 0.01312 0.41557 1.82648
5 2Q2V NAD 0.02305 0.42683 2.28311
6 4YNM SAM 0.02676 0.4082 2.28311
7 3W2E NAD 0.01951 0.44092 2.73973
8 3W2E FAD 0.01951 0.44092 2.73973
9 5MF5 C2E 0.03555 0.42061 2.73973
10 1D01 ACE MET LEU SER VAL GLU GLU GLU GLY 0.009779 0.43825 2.97619
11 4UA3 COA 0.01521 0.42628 3.09278
12 1ZPT FAD 0.01096 0.43334 3.65297
13 5KF6 NAD 0.02951 0.42418 3.65297
14 5V22 SAH 0.0148 0.42089 3.65297
15 2ODE ALF GDP 0.02895 0.42546 4.10959
16 5EOW FAD 0.02334 0.4149 4.10959
17 4JAL SAH 0.007509 0.44855 4.19162
18 5DHU 5A8 0.03479 0.44206 4.41176
19 5EOU ATP 0.04395 0.4016 4.56621
20 5CSS G3P 0.01995 0.41349 5.02283
21 5D4V SAH 0.02698 0.41262 5.02283
22 5FPE 3TR 0.01326 0.4017 5.02283
23 4GID 0GH 0.01303 0.46003 5.47945
24 5EB4 FAD 0.04178 0.41664 5.47945
25 5JFL NAD 0.01681 0.4242 5.93607
26 5LW0 AR6 0.003263 0.45982 6.06061
27 5X1M THG 0.02195 0.40517 6.84932
28 3C6K MTA 0.0392 0.40264 7.30594
29 3NUG NAD 0.004215 0.42587 8.6758
30 3PE2 E1B 0.01881 0.4046 8.6758
31 1TMM APC 0.004985 0.47105 9.49367
32 1TMM HHR 0.004741 0.47105 9.49367
33 5BVE 4VG 0.02558 0.42461 10.9589
34 4V3C C 0.01043 0.40883 19.1781
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