Receptor
PDB id Resolution Class Description Source Keywords
3FKB 1.65 Å EC: 2.7.4.6 STRUCTURE OF NDPK H122G AND TENOFOVIR-DIPHOSPHATE DICTYOSTELIUM DISCOIDEUM AN HEXAMER STRUCTURE ATP-BINDING KINASE MAGNESIUM METAL-NUCLEOTIDE METABOLISM NUCLEOTIDE-BINDING PHOSPHOPROTEIN TRANSFERASE
Ref.: NUCLEOSIDE DIPHOSPHATE KINASE AND THE ACTIVATION OF ANTIVIRAL PHOSPHONATE ANALOGS OF NUCLEOTIDES: BINDI AND PHOSPHORYLATION OF TENOFOVIR DERIVATIVES NUCLEOSIDES NUCLEOTIDES V. 28 776 2009 NUCLEIC ACIDS
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:157;
B:157;
D:158;
F:157;
F:158;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
GOL C:157;
D:157;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MG A:156;
F:156;
 Invalid;
Invalid;
 none;
none;
 submit data
24.305 Mg [Mg+2...
TNM A:160;
F:160;
 Valid;
Valid;
 none;
none;
 submit data
367.192 C9 H15 N5 O7 P2 C[C@H...
TNM MG B:160;
C:160;
E:160;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
388.476 n/a P(=O)...
TNV MG D:160;
 Valid;
 none;
 submit data
467.447 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1F3F 1.85 Å EC: 2.7.4.6 STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T- TRIPHOSPHATE.MG COMPLEX DICTYOSTELIUM DISCOIDEUM NUCLEOSIDE DIPHOSPHATE KINASE ANTI-HIV NUCLEOSIDE ANALOGUEPHOSPHORYLATION CH...O BOND TRANSFERASE
Ref.: STRUCTURAL BASIS FOR ACTIVATION OF ALPHA-BORANOPHOS NUCLEOTIDE ANALOGUES TARGETING DRUG-RESISTANT REVER TRANSCRIPTASE. EMBO J. V. 19 3520 2000
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
70% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 6XPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
17 6XPW - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
18 6XPU - IDP C10 H14 N4 O11 P2 c1nc2c(n1[....
19 6XPT - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
20 6XP7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 6XPS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
23 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
25 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
26 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
30 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
31 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
18 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
20 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
21 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
22 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
23 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
24 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
25 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
26 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
29 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
30 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
31 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
32 3EE3 - CDP MG n/a n/a
33 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 3Q86 - GTP MG n/a n/a
35 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
37 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
38 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 6XPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
40 6XPW - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
41 6XPU - IDP C10 H14 N4 O11 P2 c1nc2c(n1[....
42 6XPT - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
43 6XP7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 6XPS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
46 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
47 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
48 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
49 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
51 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
52 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
53 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
54 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
55 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
56 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
57 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TNM; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 TNM 1 1
2 EOI 0.704225 0.957143
3 TNM MG 0.676471 0.882353
4 TNV MG 0.630137 0.882353
5 ARP 0.555556 0.686567
6 APS 0.555556 0.686567
7 EMA 0.5 0.9
8 5HG 0.479452 0.857143
9 9PP 0.441558 0.869565
Ligand no: 2; Ligand: TNM MG; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 TNM MG 1 1
2 TNV MG 0.830769 1
3 TNM 0.676471 0.882353
4 EOI 0.613333 0.84507
5 ARP 0.53125 0.671875
6 APS 0.53125 0.671875
7 9PP 0.48 0.921875
8 5HG 0.44 0.771429
Ligand no: 3; Ligand: TNV MG; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 TNV MG 1 1
2 TNM MG 0.830769 1
3 TNM 0.630137 0.882353
4 EOI 0.575 0.84507
5 ARP 0.492754 0.671875
6 APS 0.492754 0.671875
7 9PP 0.45 0.921875
8 5HG 0.4125 0.771429
Similar Ligands (3D)
Ligand no: 1; Ligand: TNM; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: TNM MG; Similar ligands found: 2
No: Ligand Similarity coefficient
1 HA1 0.8766
2 9D9 0.8605
Ligand no: 3; Ligand: TNV MG; 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 : 1F3F; Ligand: D4T; 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: 1f3f.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1F3F; Ligand: D4T; 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: 1f3f.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1F3F; Ligand: D4T; 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: 1f3f.bio1) has 56 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1F3F; Ligand: D4T; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1f3f.bio1) has 56 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1F3F; Ligand: D4T; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1F3F; Ligand: D4T; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1F3F; Ligand: D4D; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1F3F; Ligand: D4D; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
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