Receptor
PDB id Resolution Class Description Source Keywords
1Z4Q 2.05 Å EC: 3.1.3.5 STRUCTURE OF THE D41N VARIANT OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH 2',3'-DIDEOXY-2',3- D IDEHYDROTHYMIDINE 5'-MONOPHOSPHATE (D4T-MP) HOMO SAPIENS ALFA BETA FOLD HYDROLASE
Ref.: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE STRUCTURE V. 13 1081 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
D4M A:1489;
 Valid;
 none;
 submit data
304.193 C10 H13 N2 O7 P CC1=C...
MG A:2001;
A:2229;
 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: D4M; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 D4M 1 1
2 D4D 0.787879 0.984615
3 D4T 0.742857 0.984615
4 2DT 0.486486 0.927536
5 TMP 0.461538 0.927536
6 NYM 0.455696 0.901408
7 FDM 0.455696 0.888889
8 THP 0.45 0.941176
9 ATM 0.423529 0.864865
10 T3P 0.410256 0.913043
11 TYD 0.4 0.914286
Similar Ligands (3D)
Ligand no: 1; Ligand: D4M; Similar ligands found: 80
No: Ligand Similarity coefficient
1 BRU 0.9594
2 5IU 0.9587
3 UFP 0.9526
4 UMP 0.9520
5 DUS 0.9494
6 DU 0.9437
7 5BU 0.9433
8 QBT 0.9425
9 U5P 0.9413
10 DCM 0.9409
11 5FU 0.9391
12 UP6 0.9371
13 5CM 0.9354
14 C5P 0.9351
15 DOC 0.9344
16 CNU 0.9339
17 AMP 0.9334
18 UMC 0.9296
19 U 0.9295
20 FNU 0.9291
21 BMP 0.9254
22 IMP 0.9250
23 TKW 0.9244
24 H2U 0.9238
25 C 0.9214
26 S5P 0.9202
27 5HU 0.9193
28 BMQ 0.9186
29 CAR 0.9180
30 FN5 0.9176
31 9L3 0.9169
32 DC 0.9165
33 NUP 0.9165
34 DDN 0.9163
35 6MA 0.9137
36 PSU 0.9119
37 5GP 0.9119
38 T3S 0.9111
39 8BR 0.9110
40 CH 0.9105
41 DA 0.9105
42 D5M 0.9105
43 DI 0.9100
44 U6M 0.9092
45 5HM 0.9051
46 QTJ 0.9046
47 C2R 0.9023
48 IRP 0.9017
49 16B 0.9003
50 8OP 0.8985
51 G 0.8976
52 NCN 0.8973
53 AS 0.8967
54 AIR 0.8964
55 TXS 0.8963
56 PFU 0.8933
57 9RK 0.8928
58 6CN 0.8918
59 AMZ 0.8901
60 DG 0.8896
61 DGP 0.8896
62 AZU 0.8886
63 FMP 0.8869
64 HDU 0.8854
65 IMU 0.8840
66 U4S 0.8809
67 IGP 0.8798
68 NMN 0.8796
69 BVP 0.8790
70 U1S 0.8763
71 U3S 0.8763
72 U2S 0.8752
73 NIA 0.8741
74 6OG 0.8731
75 TCW 0.8638
76 PZB 0.8626
77 43J 0.8624
78 O8M 0.8609
79 9X0 0.8584
80 VIB 0.8583
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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