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Receptor
PDB id Resolution Class Description Source Keywords
5EDD 1.97 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DUTPASE R140 MUTANT MYCOBACTERIUM TUBERCULOSIS JELLY-ROLL ENZYME-LIGAND COMPLEX HYDROLASE
Ref.: STRUCTURAL CHARACTERIZATION OF ARGININE FINGERS: IDENTIFICATION OF AN ARGININE FINGER FOR THE PYROPH DUTPASES. J. AM. CHEM. SOC. V. 138 15035 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:203;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
DUP A:202;
Valid;
none;
Kd = 5.7 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
TRS A:201;
Invalid;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PY4 1.49 Å EC: 3.6.1.23 FULL LENGTH STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTP COMPLEXED WITH MAGNESIUM AND ALPHA,BETA-IMIDO-DUTP. MYCOBACTERIUM TUBERCULOSIS JELLY-ROLL ENZYME-LIGAND COMPLEX HYDROLASE
Ref.: ACTIVE SITE OF MYCOBACTERIAL DUTPASE: STRUCTURAL CHARACTERISTICS AND A BUILT-IN SENSOR. BIOCHEM.BIOPHYS.RES.COMMUN. V. 373 8 2008
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3I93 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 3H6D - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
3 3HZA - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 1SNF - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
10 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1SJN - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 3I93 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
3 3H6D - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 3HZA - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
9 1SNF - UMP C9 H13 N2 O8 P C1[C@@H]([....
10 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
11 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1SJN - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
4 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
5 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
9 1SNF - UMP C9 H13 N2 O8 P 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 : 2PY4; Ligand: DUP; Similar sites found with APoc: 22
This union binding pocket(no: 1) in the query (biounit: 2py4.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
1 1GXU 2HP None
2 1XPJ TLA None
3 4U00 ADP None
4 5A96 GTP 2.40964
5 2JK0 ASP 3.38462
6 1XX6 ADP 3.44828
7 2OG2 MLI 3.44828
8 5GVR LMR 4.5977
9 1Q19 SSC 4.5977
10 5C9P FUC 4.5977
11 1WS5 MMA 6.01504
12 2AWN ADP 6.32184
13 3W5J GDP 8.04598
14 1JJ7 ADP 8.04598
15 2OBM ADP 8.62069
16 4PPF FLC 8.62069
17 2HIM ASN 12.069
18 5TSH ADP 12.6437
19 6C0B MLI 13.7931
20 5MB4 NAG 14.9425
21 2QXX TTP 24.1379
22 5Y5Q DUT 43.6782
Pocket No.: 2; Query (leader) PDB : 2PY4; 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: 2py4.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2PY4; 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: 2py4.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
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