Receptor
PDB id Resolution Class Description Source Keywords
4NFL 1.38 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUC IN COMPLEX WITH THE INHIBITOR NPB-T HOMO SAPIENS HAD-LIKE NUCLEOTIDASE MITOCHONDRIA HYDROLASE-HYDROLASE INCOMPLEX
Ref.: CONFORMATIONALLY CONSTRAINED NUCLEOSIDE PHOSPHONIC POTENT INHIBITORS OF HUMAN MITOCHONDRIAL AND CYTOSO 5'(3')-NUCLEOTIDASES. ORG.BIOMOL.CHEM. V. 12 7971 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEG A:313;
A:315;
A:316;
A:317;
A:312;
A:318;
A:314;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
GOL A:307;
A:308;
A:310;
A:309;
A:305;
A:306;
A:311;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
TRS A:304;
 Invalid;
 none;
 submit data
122.143 C4 H12 N O3 C(C(C...
2JW A:303;
 Valid;
 none;
 Ki = 22.1 uM
455.313 C17 H18 N3 O10 P CC1=C...
PO4 A:302;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
MG A:301;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4L6C 1.8 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDA COMPLEX WITH THE INHIBITOR PIB-T HOMO SAPIENS 5-prime -NUCLEOTIDASE MITOCHONDRIA PROTEIN CONFORMATION SEQUENCHOMOLOGY HAD-LIKE HYDROLASE DEPHOSPHORYLATION PHOSPHORYHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: CONFORMATIONALLY CONSTRAINED NUCLEOSIDE PHOSPHONIC POTENT INHIBITORS OF HUMAN MITOCHONDRIAL AND CYTOSO 5'(3')-NUCLEOTIDASES. ORG.BIOMOL.CHEM. V. 12 7971 2014
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
15 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
15 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 2JW; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 2JW 1 1
2 DPB 0.7875 0.884615
3 0BT 0.771084 0.841463
4 2E2 0.735632 0.884615
5 9RC 0.443396 0.903614
6 WMJ 0.438095 0.835294
Similar Ligands (3D)
Ligand no: 1; Ligand: 2JW; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4L6C; Ligand: 0BT; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4l6c.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1L5Y BEF 7.09677
2 1L5Y BEF 7.09677
Pocket No.: 2; Query (leader) PDB : 4L6C; Ligand: 0BT; 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: 4l6c.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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