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 9 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 8 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 6 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DU; Similar ligands found: 59
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 DUT MG 0.694444 0.955224
9 DUS 0.692308 0.853333
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 DC 0.561644 0.928571
20 DCM 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U 0.527778 0.911765
24 U5P 0.527778 0.911765
25 DDU 0.523077 0.753623
26 UMC 0.520548 0.941176
27 QBT 0.493333 0.927536
28 DUA 0.487805 0.783784
29 DU3 0.487805 0.780822
30 5CM 0.481013 0.890411
31 DU4 0.47619 0.76
32 TYD 0.469136 0.942857
33 YYY 0.451219 0.915493
34 UDP 0.45 0.898551
35 TTP 0.447059 0.942857
36 8OG 0.435294 0.835443
37 U2P 0.434211 0.884058
38 U3P 0.434211 0.897059
39 UA3 0.434211 0.897059
40 UTP 0.433735 0.898551
41 44P 0.43038 0.914286
42 DCP 0.430233 0.915493
43 U5F 0.428571 0.898551
44 0KX 0.425287 0.890411
45 DUX 0.411765 0.756757
46 2KH 0.411765 0.873239
47 UMF 0.410256 0.84507
48 UPU 0.409091 0.871429
49 F6G 0.409091 0.876712
50 TTP MG 0.409091 0.914286
51 139 0.409091 0.8
52 URI 0.408451 0.771429
53 TBD 0.406977 0.90411
54 DU DU DU DU BRU DA DU 0.40625 0.771084
55 PUA 0.405172 0.833333
56 UNP 0.402299 0.873239
57 UAD 0.4 0.873239
58 PUP 0.4 0.955882
59 UDX 0.4 0.873239
Similar Ligands (3D)
Ligand no: 1; Ligand: DU; Similar ligands found: 94
No: Ligand Similarity coefficient
1 C 0.9730
2 CAR 0.9723
3 C5P 0.9681
4 FDM 0.9649
5 UP6 0.9647
6 H2U 0.9629
7 DOC 0.9620
8 9L3 0.9598
9 CH 0.9596
10 FN5 0.9596
11 NYM 0.9580
12 PSU 0.9530
13 16B 0.9517
14 BMP 0.9504
15 TKW 0.9502
16 5FU 0.9490
17 5BU 0.9458
18 D4M 0.9437
19 2DT 0.9437
20 BMQ 0.9431
21 NUP 0.9400
22 U6M 0.9325
23 C2R 0.9313
24 S5P 0.9295
25 DI 0.9277
26 DA 0.9275
27 D5M 0.9275
28 AMP 0.9269
29 PFU 0.9242
30 T3S 0.9242
31 NMN 0.9234
32 NCN 0.9224
33 AIR 0.9223
34 NIA 0.9194
35 AMZ 0.9180
36 FNU 0.9175
37 IMP 0.9168
38 6MA 0.9138
39 U4S 0.9134
40 5HM 0.9130
41 ATM 0.9120
42 6CN 0.9112
43 FMP 0.9092
44 CNU 0.9077
45 AS 0.9077
46 7D5 0.9028
47 IRP 0.9020
48 MTE 0.8992
49 5GP 0.8989
50 IRN 0.8979
51 AZU 0.8977
52 5QT 0.8965
53 8BR 0.8959
54 CMP 0.8957
55 8OP 0.8950
56 DG 0.8948
57 DGP 0.8948
58 VKE 0.8917
59 6AU 0.8904
60 OMP 0.8878
61 JW5 0.8877
62 6SY 0.8869
63 GAR 0.8867
64 2T4 0.8854
65 NEC 0.8836
66 PZB 0.8833
67 71V 0.8832
68 N5O 0.8825
69 RP1 0.8825
70 G 0.8822
71 TXS 0.8794
72 GO1 0.8790
73 XMP 0.8768
74 SP1 0.8761
75 TWB 0.8748
76 CDP 0.8746
77 MTA 0.8718
78 MTH 0.8714
79 8GM 0.8663
80 15I 0.8654
81 3N4 0.8651
82 CC7 0.8650
83 IGP 0.8638
84 MTM 0.8634
85 VIB 0.8625
86 6G7 0.8611
87 CTN 0.8597
88 1CE 0.8583
89 4X2 0.8582
90 DCZ 0.8572
91 FAI 0.8570
92 9RK 0.8558
93 F95 0.8547
94 22T 0.8531
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D3Y; Ligand: DU; 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: 2d3y.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
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