Receptor
PDB id Resolution Class Description Source Keywords
1LWX 2.3 Å EC: 2.7.4.6 AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE DICTYOSTELIUM DISCOIDEUM PHOSPHOTRANSFERASE ANTIVIRAL AGENT AZIDOTHYMIDINE
Ref.: X-RAY ANALYSIS OF AZIDO-THYMIDINE DIPHOSPHATE BINDI NUCLEOSIDE DIPHOSPHATE KINASE. PROC.NATL.ACAD.SCI.USA V. 94 7162 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AZD A:156;
B:156;
C:156;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
427.201 C10 H15 N5 O10 P2 CC1=C...
MG A:157;
C:157;
 Invalid;
Invalid;
 none;
none;
 submit data
24.305 Mg [Mg+2...
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: AZD; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 AZD 1 1
2 ATM 0.813333 0.986667
3 ABT 0.783133 0.974026
4 AZZ 0.693333 0.868421
5 TYD 0.654321 0.907895
6 ATY 0.609195 0.884615
7 TTP 0.586207 0.907895
8 TMP 0.535714 0.894737
9 Z5A 0.516667 0.837209
10 NYM 0.511628 0.896104
11 FDM 0.511628 0.860759
12 D3T 0.511111 0.907895
13 T3P 0.506024 0.881579
14 THP 0.505747 0.906667
15 DAU 0.490196 0.85
16 TLO 0.484848 0.860759
17 TDX 0.480392 0.860759
18 1JB 0.480392 0.85
19 18T 0.480392 0.85
20 TRH 0.480392 0.85
21 TTP MG 0.478723 0.881579
22 0FX 0.47619 0.851852
23 LLT 0.475 0.792208
24 THM 0.475 0.792208
25 T3F 0.471154 0.851852
26 T3Q 0.471154 0.851852
27 2DT 0.470588 0.894737
28 QDM 0.46729 0.841463
29 T46 0.466667 0.85
30 3R2 0.466019 0.839506
31 9RC 0.465347 0.845238
32 FNF 0.462963 0.8625
33 1YF 0.462963 0.8625
34 TBD 0.462366 0.897436
35 MMF 0.462264 0.851852
36 TPE 0.461538 0.839506
37 D4D 0.461538 0.866667
38 4TG 0.458716 0.8625
39 DWN 0.457143 0.851852
40 3YN 0.457143 0.85
41 0N2 0.45283 0.841463
42 JHZ 0.449541 0.831325
43 0DN 0.445783 0.75641
44 AKM 0.436364 0.833333
45 DUD 0.419355 0.868421
46 FUH 0.418803 0.851852
47 QUH 0.418803 0.851852
48 D4T 0.412371 0.866667
49 TXS 0.406593 0.740741
50 T5A 0.404959 0.793103
Similar Ligands (3D)
Ligand no: 1; Ligand: AZD; Similar ligands found: 3
No: Ligand Similarity coefficient
1 UDP 0.8849
2 YYY 0.8779
3 CDP 0.8684
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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