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 (2D)
Ligand no: 1; Ligand: BVP; Similar ligands found: 53
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 TMP 0.64 0.957747
6 5HU 0.64 0.944444
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 DDN 0.5 0.942857
12 TTP 0.5 0.944444
13 TBD 0.477273 0.906667
14 DC 0.464286 0.878378
15 DCM 0.464286 0.878378
16 TTP MG 0.461538 0.916667
17 FDM 0.458824 0.918919
18 5CM 0.448276 0.893333
19 NYM 0.44186 0.931507
20 TLO 0.438776 0.893333
21 LLT 0.435897 0.821918
22 THM 0.435897 0.821918
23 TDX 0.435644 0.893333
24 3R2 0.435644 0.87013
25 9RC 0.434343 0.807229
26 DUD 0.431818 0.929577
27 DAU 0.431373 0.881579
28 ID2 0.43038 0.8
29 UMC 0.428571 0.888889
30 T3F 0.427184 0.858974
31 T3Q 0.427184 0.858974
32 QBT 0.423529 0.876712
33 18T 0.421569 0.881579
34 1JB 0.421569 0.881579
35 TRH 0.421569 0.881579
36 THP 0.420455 0.943662
37 UC5 0.41573 0.916667
38 3YN 0.413462 0.881579
39 DWN 0.413462 0.858974
40 DUT 0.413043 0.929577
41 ATM 0.413043 0.87013
42 QDM 0.411215 0.848101
43 0N2 0.409524 0.848101
44 T46 0.409524 0.881579
45 DUP 0.408602 0.90411
46 0DN 0.407407 0.833333
47 FNF 0.407407 0.87013
48 1YF 0.407407 0.87013
49 AKM 0.407407 0.839506
50 DUN 0.406593 0.90411
51 MMF 0.40566 0.858974
52 0FX 0.40566 0.858974
53 4TG 0.40367 0.87013
Similar Ligands (3D)
Ligand no: 1; Ligand: BVP; Similar ligands found: 29
No: Ligand Similarity coefficient
1 8OG 0.9322
2 5FU 0.9267
3 CNU 0.9219
4 G 0.9181
5 8GM 0.9108
6 AS 0.9101
7 5BU 0.9085
8 5GP 0.9055
9 AMP 0.9052
10 2DT 0.9015
11 T3S 0.9007
12 8OP 0.8980
13 FNU 0.8970
14 XMP 0.8952
15 NMN 0.8907
16 NCN 0.8900
17 DG 0.8897
18 DGP 0.8875
19 TKW 0.8865
20 DA 0.8861
21 6MA 0.8839
22 IMP 0.8810
23 D5M 0.8809
24 D4M 0.8790
25 8BR 0.8647
26 C2R 0.8590
27 TXS 0.8576
28 Z8B 0.8548
29 NIA 0.8521
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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