Receptor
PDB id Resolution Class Description Source Keywords
2JAW 1.95 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF D41N VARIANT OF HUMAN MITOCHONDRIAL 5'( DEOXYRIBONUCLEOTIDASE (MDN) IN COMPLEX WITH 5-BROMOVINYLDEO5 '-MONOPHOSPHATE HOMO SAPIENS TRANSIT PEPTIDE NUCLEOTIDE-BINDING MITOCHONDRIAL METAL-BIALFA BETA FOLD NUCLEOTIDE- BINDING NUCLEOTIDE METABOLISMHYDROLASE MAGNESIUM MITOCHONDRION
Ref.: CRYSTAL STRUCTURES OF HUMAN AND MURINE DEOXYRIBONUCLEOTIDASES: INSIGHTS INTO RECOGNITION O SUBSTRATES AND NUCLEOTIDE ANALOGUES. BIOCHEMISTRY V. 46 13809 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BVP A:1228;
Valid;
none;
submit data
413.115 C11 H14 Br N2 O8 P C1[C@...
MG A:1229;
A:1230;
Part of Protein;
Part of Protein;
none;
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
Ligand no: 1; Ligand: BVP; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 BVP 1 1
2 BVD 0.735294 0.861111
3 BRU 0.662162 0.958333
4 UFP 0.648649 0.931507
5 5HU 0.64 0.944444
6 TMP 0.64 0.957747
7 5IU 0.631579 0.931507
8 DU 0.531646 0.942857
9 UMP 0.531646 0.942857
10 TYD 0.52381 0.944444
11 TTP 0.5 0.944444
12 DDN 0.5 0.942857
13 TBD 0.477273 0.906667
14 DCM 0.464286 0.878378
15 DC 0.464286 0.878378
16 TTP MG 0.461538 0.916667
17 FDM 0.458824 0.918919
18 NYM 0.44186 0.931507
19 TLO 0.438776 0.893333
20 THM 0.435897 0.821918
21 LLT 0.435897 0.821918
22 TDX 0.435644 0.893333
23 3R2 0.435644 0.87013
24 9RC 0.434343 0.807229
25 DUD 0.431818 0.929577
26 DAU 0.431373 0.881579
27 ID2 0.43038 0.8
28 UMC 0.428571 0.888889
29 T3F 0.427184 0.858974
30 T3Q 0.427184 0.858974
31 DT DT DT 0.424242 0.891892
32 QBT 0.423529 0.876712
33 TRH 0.421569 0.881579
34 1JB 0.421569 0.881579
35 18T 0.421569 0.881579
36 THP 0.420455 0.943662
37 DT DT DT DT DT 0.417476 0.918919
38 UC5 0.41573 0.916667
39 DWN 0.413462 0.858974
40 3YN 0.413462 0.881579
41 DUT 0.413043 0.929577
42 ATM 0.413043 0.87013
43 QDM 0.411215 0.848101
44 0N2 0.409524 0.848101
45 T46 0.409524 0.881579
46 DUP 0.408602 0.90411
47 AKM 0.407407 0.839506
48 0DN 0.407407 0.833333
49 FNF 0.407407 0.87013
50 1YF 0.407407 0.87013
51 DUN 0.406593 0.90411
52 0FX 0.40566 0.858974
53 MMF 0.40566 0.858974
54 4TG 0.40367 0.87013
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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