Receptor
PDB id Resolution Class Description Source Keywords
1SNF 1.85 Å EC: 3.6.1.23 MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM DEOXYURIDINE 5'-MONOPHOSPHATE MYCOBACTERIUM TUBERCULOSIS JELLY-ROLL STRUCTURAL GENOMICS PSI PROTEIN STRUCTURE INITTB STRUCTURAL GENOMICS CONSORTIUM TBSGC HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS INSIGHTS INTO THE CATALYTIC MECHANISM. J.MOL.BIOL. V. 341 503 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:2171;
B:3171;
C:1171;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
NO3 A:2172;
B:3172;
C:1172;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.005 N O3 [N+](...
TRS B:3173;
B:3174;
Invalid;
Invalid;
none;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
UMP A:1170;
B:2170;
C:3170;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
308.182 C9 H13 N2 O8 P C1[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: UMP; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 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 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2py4.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
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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