Receptor
PDB id Resolution Class Description Source Keywords
5MYD 2.3 Å EC: 3.6.1.23 CONVERGENT EVOLUTION INVOLVING DIMERIC AND TRIMERIC DUTPASES SIGNALLING. STAPHYLOCOCCUS SP. HMSC068C09 STAPHYLOCOCCUS AUREUS PATHOGENICITY ISLAND SAPI DUTPASESSIGNALLING GENE TRANSFER MOBILE GENETIC ELEMENTS HYDROLA
Ref.: CONVERGENT EVOLUTION INVOLVING DIMERIC AND TRIMERIC IN PATHOGENICITY ISLAND MOBILIZATION. PLOS PATHOG. V. 13 06581 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUP C:201;
A:201;
B:201;
D:201;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 ic50 = 13.9 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
MG C:202;
D:202;
C:203;
A:203;
B:203;
D:203;
B:202;
A:202;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
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
5MYD 2.3 Å EC: 3.6.1.23 CONVERGENT EVOLUTION INVOLVING DIMERIC AND TRIMERIC DUTPASES SIGNALLING. STAPHYLOCOCCUS SP. HMSC068C09 STAPHYLOCOCCUS AUREUS PATHOGENICITY ISLAND SAPI DUTPASESSIGNALLING GENE TRANSFER MOBILE GENETIC ELEMENTS HYDROLA
Ref.: CONVERGENT EVOLUTION INVOLVING DIMERIC AND TRIMERIC IN PATHOGENICITY ISLAND MOBILIZATION. PLOS PATHOG. V. 13 06581 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 5MYD ic50 = 13.9 uM 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 271 families.
1 5MYD ic50 = 13.9 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5MIL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 5MYD ic50 = 13.9 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5MIL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DUP; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 DU 0.742857 0.956522
4 UMP 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUT MG 0.62963 0.914286
9 0KX 0.614458 0.931507
10 DUS 0.6 0.820513
11 UMP AF3 PO4 0.595238 0.842105
12 DUR 0.585714 0.842857
13 2KH 0.585366 0.915493
14 UM3 0.506329 0.914286
15 DU DU DU DU BRU DU DU 0.495238 0.831169
16 DDN 0.47561 0.956522
17 DU4 0.472527 0.730769
18 BRU 0.458824 0.891892
19 DDU 0.453333 0.722222
20 DU3 0.450549 0.773333
21 DUA 0.450549 0.776316
22 TYD 0.449438 0.930556
23 UFP 0.447059 0.891892
24 TMP 0.44186 0.916667
25 5HU 0.44186 0.930556
26 5IU 0.436782 0.891892
27 UNP 0.434783 0.915493
28 YYY 0.433333 0.90411
29 UDP 0.431818 0.887324
30 TTP 0.430108 0.930556
31 DCM 0.425287 0.890411
32 DC 0.425287 0.890411
33 UTP 0.417582 0.887324
34 DCP 0.414894 0.90411
35 U5F 0.413043 0.887324
36 U 0.411765 0.873239
37 U5P 0.411765 0.873239
38 BVP 0.408602 0.90411
39 DZ4 0.40404 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: DUP; Similar ligands found: 14
No: Ligand Similarity coefficient
1 MG TTP 0.9430
2 ANP 0.9039
3 7D4 0.8940
4 FZQ 0.8841
5 2TM 0.8798
6 CTP 0.8797
7 ATP 0.8755
8 FZK 0.8750
9 3AT 0.8719
10 HF4 0.8636
11 AHX 0.8630
12 AGS 0.8579
13 ACP 0.8558
14 8DG 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5MYD; Ligand: DUP; 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: 5myd.bio4) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5myd.bio4) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5myd.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5myd.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5myd.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5myd.bio3) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5myd.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5MYD; Ligand: DUP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5myd.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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