Receptor
PDB id Resolution Class Description Source Keywords
1F6T 1.92 Å EC: 2.7.4.6 STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO( COMPLEX DICTYOSTELIUM DISCOIDEUM NUCLEOSIDE DIPHOSPHATE KINASE ANTI-HIV NUCLEOSIDE ANALOGUEPHOSPHORYLATION BORANOPHOSPHATE TRANSFERASE
Ref.: STRUCTURAL BASIS FOR ACTIVATION OF ALPHA-BORANOPHOS NUCLEOTIDE ANALOGUES TARGETING DRUG-RESISTANT REVER TRANSCRIPTASE. EMBO J. V. 19 3520 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:163;
B:164;
C:165;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
TBD A:160;
B:161;
C:162;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
400.024 C10 H19 B N2 O10 P2 [BH3-...
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: TBD; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 TBD 1 1
2 TMP 0.708333 0.945205
3 TYD 0.662338 0.958904
4 TTP 0.62963 0.958904
5 THM 0.623188 0.837838
6 LLT 0.623188 0.837838
7 0DN 0.583333 0.8
8 TTP MG 0.583333 0.931507
9 TLO 0.549451 0.907895
10 T3P 0.545455 0.905405
11 9RC 0.543478 0.821429
12 DAU 0.536842 0.896104
13 TDX 0.526316 0.907895
14 1JB 0.526316 0.896104
15 18T 0.526316 0.896104
16 3R2 0.526316 0.884615
17 TRH 0.526316 0.896104
18 T46 0.525773 0.896104
19 TXS 0.525 0.759494
20 0FX 0.520408 0.873418
21 DWN 0.515464 0.873418
22 T3F 0.515464 0.873418
23 3YN 0.515464 0.896104
24 T3Q 0.515464 0.873418
25 NYM 0.512195 0.92
26 FDM 0.512195 0.883117
27 T3S 0.512195 0.759494
28 0N2 0.510204 0.8625
29 QDM 0.51 0.8625
30 UFP 0.506173 0.87013
31 THP 0.506024 0.931507
32 MMF 0.50505 0.873418
33 5HU 0.5 0.932432
34 BRU 0.5 0.87013
35 ATM 0.494253 0.884615
36 5IU 0.493976 0.87013
37 JHZ 0.490196 0.851852
38 FNF 0.490196 0.884615
39 1YF 0.490196 0.884615
40 AKM 0.490196 0.853659
41 4TG 0.485437 0.884615
42 3DR DT DT DT DT DT 0.485437 0.894737
43 BVP 0.477273 0.906667
44 ATY 0.472527 0.907895
45 AZD 0.462366 0.897436
46 AZZ 0.457831 0.772152
47 FUH 0.454545 0.873418
48 QUH 0.454545 0.873418
49 T5A 0.451327 0.811765
50 2DT 0.451219 0.918919
51 DT ME6 DT 0.45045 0.860759
52 WMJ 0.443299 0.755814
53 4TA 0.42735 0.8
54 ABT 0.42 0.923077
55 5CM 0.41573 0.883117
56 D3T 0.413043 0.932432
57 ID2 0.4125 0.769231
58 DU 0.406977 0.90411
59 UMP 0.406977 0.90411
60 O5W 0.404959 0.813953
61 BVD 0.404762 0.802632
62 TPE 0.403846 0.860759
63 ADS THS THS THS 0.401639 0.752809
64 7SG 0.401575 0.833333
65 TQP 0.401575 0.833333
Similar Ligands (3D)
Ligand no: 1; Ligand: TBD; Similar ligands found: 13
No: Ligand Similarity coefficient
1 YYY 0.9804
2 DUD 0.9720
3 CDP 0.9634
4 UDP 0.9623
5 D4D 0.9526
6 DGI 0.9380
7 CDP MG 0.9375
8 ADP 0.9046
9 GDP 0.8937
10 IDP 0.8745
11 D4T 0.8700
12 U5P 0.8568
13 ADX 0.8528
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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