Receptor
PDB id Resolution Class Description Source Keywords
6XPU 1.9 Å EC: 2.7.4.6 NUCLEOSIDE DIPHOSPHATE KINASE FROM ASPERGILLUS FUMGIATUS AF2 TO IDP ASPERGILLUS FUMIGATUS AF293 NUCLEOSIDE DIPHOSPHATE KINASE PHOSPHOTRANSFERASE KINASE TRANSFERASE
Ref.: NUCLEOSIDE SELECTIVITY OF ASPERGILLUS FUMIGATUS NUCLEOSIDE-DIPHOSPHATE KINASE. FEBS J. 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:201;
B:201;
C:201;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
IDP C:202;
A:202;
B:202;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
428.186 C10 H14 N4 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6XPS 1.64 Å EC: 2.7.4.6 NUCLEOSIDE DIPHOSPHATE KINASE FROM ASPERGILLUS FUMGIATUS AF2 TO GDP ASPERGILLUS FUMIGATUS AF293 NUCLEOSIDE DIPHOSPHATE KINASE PHOSPHOTRANSFERASE KINASE TRANSFERASE
Ref.: NUCLEOSIDE SELECTIVITY OF ASPERGILLUS FUMIGATUS NUCLEOSIDE-DIPHOSPHATE KINASE. FEBS J. 2020
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 6XPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 6XPW - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
3 6XPU - IDP C10 H14 N4 O11 P2 c1nc2c(n1[....
4 6XPT - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 6XP7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 6XPS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
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: IDP; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 IDP 1 1
2 IMP 0.824324 0.986111
3 R7I 0.822785 0.972603
4 R5I 0.822785 0.972603
5 NOS 0.675676 0.849315
6 GDP 0.632184 0.972973
7 GTP 0.576087 0.972973
8 GP3 0.549451 0.947368
9 GNH 0.537634 0.96
10 9GM 0.53125 0.947368
11 GNP 0.53125 0.947368
12 GCP 0.520833 0.947368
13 G1R 0.520833 0.96
14 GSP 0.515464 0.923077
15 G 0.505495 0.959459
16 5GP 0.505495 0.959459
17 SIB 0.505155 0.7625
18 GAV 0.50505 0.935065
19 PRT 0.5 0.986111
20 GDD 0.495238 0.935065
21 GDC 0.495238 0.935065
22 GKE 0.495238 0.935065
23 GMV 0.494845 0.947368
24 CZF 0.494737 0.958904
25 DI 0.494505 0.907895
26 G2R 0.490196 0.935065
27 G2P 0.484848 0.935065
28 ADP 0.483516 0.918919
29 GKD 0.477064 0.935065
30 JB2 0.477064 0.935065
31 GDR 0.476636 0.935065
32 GFB 0.476636 0.935065
33 6CK 0.472222 0.911392
34 GPG 0.471154 0.935065
35 G5P 0.46789 0.947368
36 Y9Z 0.46729 0.878049
37 GP2 0.463918 0.935065
38 GTG 0.462963 0.911392
39 GDP BEF 0.46 0.909091
40 GDX 0.459459 0.947368
41 G3A 0.458716 0.947368
42 ITT 0.457447 0.891892
43 G3D 0.455446 0.959459
44 GTP MG 0.455446 0.933333
45 ALF 5GP 0.45 0.864198
46 SNI 0.447059 0.813333
47 7DD 0.446809 0.905405
48 G4P 0.446602 0.959459
49 GPD 0.446429 0.9
50 6AD 0.444444 0.839506
51 YGP 0.444444 0.876543
52 QBQ 0.444444 0.959459
53 JB3 0.439655 0.923077
54 GDP ALF 0.438095 0.864198
55 GDP AF3 0.438095 0.864198
56 HEJ 0.4375 0.918919
57 ATP 0.4375 0.918919
58 AQP 0.43299 0.918919
59 6SW 0.43299 0.917808
60 5FA 0.43299 0.918919
61 93A 0.431579 0.853659
62 NO7 0.431373 0.883117
63 CAG 0.42623 0.857143
64 MGP 0.425743 0.935065
65 HFD 0.424242 0.871795
66 JSQ 0.424242 0.871795
67 U2G 0.423729 0.911392
68 NGD 0.423729 0.935065
69 6G0 0.421569 0.935065
70 AP5 0.421053 0.893333
71 B4P 0.421053 0.893333
72 ANP 0.42 0.894737
73 A2D 0.419355 0.893333
74 0O2 0.416667 0.959459
75 AT4 0.416667 0.883117
76 2MD 0.413223 0.86747
77 MD1 0.412698 0.86747
78 M33 0.412371 0.881579
79 FEG 0.411765 0.855422
80 BA3 0.410526 0.893333
81 ZGP 0.408333 0.845238
82 MGO 0.407767 0.8625
83 6YZ 0.407767 0.894737
84 ACQ 0.405941 0.894737
85 DGI 0.405941 0.897436
86 CG2 0.404959 0.911392
87 7DT 0.40404 0.905405
88 GDP 7MG 0.403509 0.886076
89 MGD 0.403226 0.86747
90 AN2 0.402062 0.906667
91 GPX 0.401869 0.92
92 C2R 0.4 0.905405
Similar Ligands (3D)
Ligand no: 1; Ligand: IDP; Similar ligands found: 40
No: Ligand Similarity coefficient
1 ADX 0.9446
2 SON 0.9392
3 CDP 0.9252
4 A12 0.9234
5 GAP 0.9225
6 AU1 0.9204
7 AP2 0.9200
8 GJV 0.9166
9 TYD 0.9166
10 UDP 0.9155
11 CUU 0.9091
12 YYY 0.9078
13 ADP MG 0.9075
14 PRX 0.9066
15 BEF ADP 0.9003
16 6RE 0.8968
17 J7C 0.8967
18 DAT 0.8963
19 GDP MG 0.8963
20 M7G 0.8945
21 8LE 0.8940
22 CDP MG 0.8939
23 SAH 0.8930
24 AMP 0.8918
25 SAM 0.8910
26 CA0 0.8889
27 KG4 0.8888
28 DUD 0.8882
29 8GD 0.8816
30 TBD 0.8745
31 FMP 0.8724
32 AGS 0.8674
33 AMZ 0.8657
34 ACP 0.8650
35 8OP 0.8648
36 5AL 0.8644
37 AS 0.8591
38 DTP 0.8579
39 SRP 0.8567
40 DGT 0.8537
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6XPS; Ligand: GDP; 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: 6xps.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6XPS; Ligand: GDP; 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: 6xps.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6XPS; Ligand: GDP; 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: 6xps.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6XPS; Ligand: GDP; 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: 6xps.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6XPS; Ligand: GDP; 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: 6xps.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6XPS; Ligand: GDP; 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: 6xps.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
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