Receptor
PDB id Resolution Class Description Source Keywords
4YGM 1.85 Å EC: 3.2.2.27 VACCINIA VIRUS HIS-D4/A20(1-50) IN COMPLEX WITH URACIL VACCINIA VIRUS (STRAIN COPENHAGEN) URACIL DNA GLYCOSIDASE VIRUS REPLICATION HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE IN COMPLEX WITH DNA. J.BIOL.CHEM. V. 290 17923 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:303;
B:301;
B:304;
A:302;
A:301;
B:302;
B:303;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
URA B:305;
A:304;
Valid;
Valid;
none;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YGM 1.85 Å EC: 3.2.2.27 VACCINIA VIRUS HIS-D4/A20(1-50) IN COMPLEX WITH URACIL VACCINIA VIRUS (STRAIN COPENHAGEN) URACIL DNA GLYCOSIDASE VIRUS REPLICATION HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE IN COMPLEX WITH DNA. J.BIOL.CHEM. V. 290 17923 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4YGM - URA C4 H4 N2 O2 C1=CNC(=O)....
70% 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 4YGM - URA C4 H4 N2 O2 C1=CNC(=O)....
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 4YGM - URA C4 H4 N2 O2 C1=CNC(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YGM; Ligand: URA; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 4ygm.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XG5 NAP 0.01616 0.42452 1.2931
2 2Q2V NAD 0.03658 0.40158 1.2931
3 5KHM XNH 0.01338 0.45118 1.5748
4 3OID NDP 0.02312 0.41247 1.72414
5 3AFN NAP 0.03259 0.40564 3.44828
6 5L95 AMP 0.01644 0.40924 3.84615
7 4R4U COA 0.008781 0.43266 3.87931
8 3HMO STU 0.04511 0.40291 3.87931
9 2I4I AMP 0.01407 0.41849 4.31034
10 5H9I XAN 0.000000001688 0.63217 5.17241
11 1P0F NAP 0.03891 0.40727 6.46552
12 3HGM ATP 0.007516 0.43138 6.80272
13 4IDC NDP 0.03348 0.40766 7.75862
14 4IDC 1XX 0.03348 0.40766 7.75862
15 2ZAT NAP 0.01282 0.43862 8.62069
16 1N5D NDP 0.02165 0.40462 8.62069
17 1UI0 URA 0.000000658 0.57916 9.26829
18 5G3U ITW 0.01839 0.40675 9.61539
19 4XQC NAD 0.04098 0.40109 9.61539
20 4ZFL 4NK 0.01886 0.42102 11.1111
21 4BTI 7R9 0.01603 0.41676 11.5385
22 1FIW PBZ 0.01299 0.41548 11.5385
23 3QWI CUE 0.04717 0.40153 11.5385
24 4LI4 AMP 0.003153 0.43434 12.5
25 3BJK CIT 0.009876 0.44731 13.7255
26 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.01544 0.40792 15.3846
27 4N8I COA 0.03696 0.40855 17.3077
28 3MBI HSX 0.01171 0.40601 17.3077
29 2JKY 5GP 0.01174 0.42022 19.2308
30 5L0U 660 0.01632 0.40808 21.1538
31 1EWJ BLM 0.03738 0.41468 23.0159
32 1O94 AMP 0.0157 0.41922 23.0769
33 5WGR FAD 0.01995 0.4136 26.9231
34 2EUG URA 0.000007284 0.51891 28.3843
35 3FCI 3FI 0.000008569 0.55265 30.9417
36 4WS6 WBU 0.000000007831 0.72291 34.874
37 1UDH URA 0.000001124 0.59543 38.7931
Pocket No.: 2; Query (leader) PDB : 4YGM; Ligand: URA; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 4ygm.bio2) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5G4R LF1 0.02712 0.40528 None
2 1O97 AMP 0.04162 0.42697 3.01724
3 1O97 FAD 0.04162 0.42697 3.01724
4 5FJN FAD 0.02895 0.41983 4.31034
5 5FJN BE2 0.03072 0.41983 4.31034
6 3NW7 LGV 0.0477 0.40041 5.76923
7 1YQC GLV 0.003025 0.40109 5.88235
8 4E5N NAD 0.03631 0.40011 6.03448
9 5LWY OLA 0.007965 0.40089 7.32759
10 5L4S 6KX 0.03506 0.40107 7.75862
11 5L4S NAP 0.03506 0.40107 7.75862
12 5HSA FAS 0.0256 0.40104 10.3448
13 2WDQ TEO 0.01762 0.40074 13.1783
14 1YB5 NAP 0.0428 0.4041 13.3621
15 1SW0 PGA 0.01485 0.41204 13.4615
16 5LJ0 6XX 0.01737 0.4118 23.0769
17 5D6J ATP 0.0467 0.4004 32.6923
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