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Receptor
PDB id Resolution Class Description Source Keywords
1MN7 2.15 Å EC: 2.7.4.6 NDP KINASE MUTANT (H122G;N119S;F64W) IN COMPLEX WITH ABAZTTP DICTYOSTELIUM DISCOIDEUM NDP KINASE-ABAZTTP COMPLEX TRANSFERASE
Ref.: IMPROVING NUCLEOSIDE DIPHOSPHATE KINASE FOR ANTIVIR NUCLEOTIDE ANALOGS ACTIVATION J.BIOL.CHEM. V. 277 39953 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ABT A:1160;
B:2160;
Valid;
Valid;
none;
none;
submit data
503.001 C10 H17 B N5 O12 P3 B=P(O...
MG A:1165;
B:2165;
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 10 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 (25)
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 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
17 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
19 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
20 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (51)
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 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
40 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
42 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
43 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
45 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
46 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
47 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
48 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
51 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ABT; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 ABT 1 1
2 AZD 0.783133 0.974026
3 ATM 0.753086 0.961039
4 AZZ 0.621951 0.846154
5 TTP 0.531915 0.884615
6 TYD 0.521739 0.884615
7 ATY 0.489796 0.8625
8 TMP 0.483516 0.871795
9 Z5A 0.480315 0.818182
10 FDM 0.478261 0.839506
11 NYM 0.478261 0.873418
12 THP 0.473118 0.883117
13 D3T 0.463918 0.884615
14 T3P 0.455556 0.858974
15 THM 0.425287 0.772152
16 LLT 0.425287 0.772152
17 2DT 0.423913 0.871795
18 DAU 0.423423 0.829268
19 TBD 0.42 0.923077
20 QDM 0.417391 0.821429
21 TLO 0.416667 0.839506
22 D4T 0.415842 0.844156
23 TDX 0.414414 0.839506
24 1JB 0.414414 0.829268
25 TRH 0.414414 0.829268
26 18T 0.414414 0.829268
27 JHZ 0.413793 0.811765
28 0FX 0.412281 0.831325
29 DWN 0.40708 0.831325
30 T3F 0.40708 0.831325
31 T3Q 0.40708 0.831325
32 D4D 0.40404 0.844156
33 T46 0.403509 0.829268
34 3R2 0.401786 0.819277
35 1YF 0.401709 0.841463
36 FNF 0.401709 0.841463
37 0DN 0.4 0.7375
38 MMF 0.4 0.831325
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: 3
This union binding pocket(no: 1) in the query (biounit: 1f3f.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 3QDW A2G 2.0979
2 1OYJ GSH 4.51613
3 3MBC NAP 10.9677
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: 1
This union binding pocket(no: 3) in the query (biounit: 1f3f.bio1) has 56 residues
No: Leader PDB Ligand Sequence Similarity
1 3QDV A2G 2.0979
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: 4
This union binding pocket(no: 5) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 1PTR PRB None
2 3QDX A2G GAL 2.0979
3 3QDT A2G GAL 2.0979
4 1NF8 BOG 3.22581
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: 5
This union binding pocket(no: 7) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 1PTR PRB None
2 3QDV A2G 2.0979
3 3QDX A2G GAL 2.0979
4 3QDT A2G GAL 2.0979
5 1NF8 BOG 3.22581
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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