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Receptor
PDB id Resolution Class Description Source Keywords
3B6B 2 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF ACANTHAMOEBA POLYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DGDP ACANTHAMOEBA POLYPHAGA MIMIVIRUS NDK PHOSPHOTRANSFERASE NUCLEOTIDE BINDING PROTEIN ATP- BINDING KINASE MAGNESIUM METAL-BINDING NUCLEOTIDE METABOLISM NUCLEOTIDE-BINDING PHOSPHORYLATION
Ref.: DISSECTING THE UNIQUE NUCLEOTIDE SPECIFICITY OF MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE. J.VIROL. V. 83 7142 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DGI A:139;
C:141;
E:143;
F:144;
B:140;
D:142;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
427.201 C10 H15 N5 O10 P2 c1nc2...
MG A:138;
C:138;
E:138;
F:138;
B:138;
D:138;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EM1 1.5 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF THE MIMIVIRUS NDK +KPN-N62L DOUBLE MUTANT COMPLEXED WITH DTDP ACANTHAMOEBA POLYPHAGA MIMIVIRUS PHOSPHOTRANSFERASE NUCLEOTIDE BINDING ATP-BINDING KINASE MAGNESIUM METAL-BINDING NUCLEOTIDE METABOLISM NUCLEOTIDE-BINDING PHOSPHOPROTEIN TRANSFERASE
Ref.: DISSECTING THE UNIQUE NUCLEOTIDE SPECIFICITY OF MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE. J.VIROL. V. 83 7142 2009
Members (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
3 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
7 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
8 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
10 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
11 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
13 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
15 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
17 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
18 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
20 3EE3 - CDP MG n/a n/a
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
3 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
7 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
8 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
9 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
10 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
11 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
12 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
13 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
15 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
17 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
18 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
20 3EE3 - CDP MG n/a n/a
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: DGI; Similar ligands found: 98
No: Ligand ECFP6 Tc MDL keys Tc
1 DGI 1 1
2 DGT 0.897436 1
3 DG 0.815789 0.986842
4 DGP 0.815789 0.986842
5 DG DG 0.684783 0.91358
6 GDP 0.636364 0.923077
7 CGP 0.622642 0.914634
8 G3D 0.619565 0.935065
9 G4P 0.606383 0.935065
10 GH3 0.595745 0.948052
11 GTP 0.580645 0.923077
12 DC DG 0.572727 0.891566
13 GPX 0.56701 0.922078
14 GP3 0.554348 0.9
15 0O2 0.55 0.935065
16 GNH 0.542553 0.911392
17 DAT 0.538462 0.909091
18 9GM 0.536082 0.9
19 GNP 0.536082 0.9
20 5GP 0.527473 0.910256
21 G 0.527473 0.910256
22 GCP 0.525773 0.924051
23 G1R 0.525773 0.911392
24 GAV 0.525253 0.888889
25 G2R 0.524752 0.961538
26 GSP 0.520408 0.878049
27 DI 0.516484 0.960526
28 G2P 0.50505 0.936709
29 BGO 0.504425 0.878049
30 GMV 0.5 0.9
31 GPD 0.490909 0.902439
32 2GP 0.48913 0.935065
33 3GP 0.48913 0.897436
34 GDC 0.485981 0.888889
35 GDD 0.485981 0.888889
36 GKE 0.485981 0.888889
37 HF7 0.484848 0.897436
38 ALF 5GP 0.484848 0.823529
39 GP2 0.484536 0.936709
40 DTP 0.484536 0.909091
41 P2G 0.478723 0.860759
42 GPG 0.47619 0.888889
43 3PD UM3 0.474138 0.86747
44 G5P 0.472727 0.9
45 Y9Z 0.472222 0.880952
46 GMP 0.471264 0.810127
47 ALF GDP 0.471154 0.823529
48 GDP ALF 0.471154 0.823529
49 P1G 0.46875 0.873418
50 JB2 0.468468 0.888889
51 GTG 0.46789 0.86747
52 GFB 0.46789 0.888889
53 GDR 0.46789 0.888889
54 DG DC 0.467742 0.925926
55 G3A 0.463636 0.9
56 6CK 0.463636 0.86747
57 DG DA DC DG 0.459854 0.880952
58 GCP G 0.457944 0.873418
59 GDP AF3 0.457143 0.823529
60 GKD 0.455357 0.888889
61 GDX 0.451327 0.9
62 YGP 0.449541 0.835294
63 JB3 0.444444 0.878049
64 CF2 0.44186 0.802326
65 GGM 0.441667 0.857143
66 DA DU DG DA 0.440678 0.835294
67 NGD 0.440678 0.888889
68 8GD 0.44 0.857143
69 CAG 0.430894 0.818182
70 U2G 0.428571 0.86747
71 G G 0.428571 0.876543
72 3ZE 0.424242 0.886076
73 DA DC DG DA 0.423611 0.914634
74 DC DG DA DC 0.423358 0.902439
75 CG2 0.421488 0.86747
76 GDP 7MG 0.421053 0.843373
77 SGP 0.418367 0.807229
78 2MD 0.418033 0.827586
79 MD1 0.417323 0.848837
80 FEG 0.416667 0.858824
81 DU DU DU DU BRU DG DU 0.416667 0.818182
82 DA 0.414894 0.883117
83 DUD 0.414894 0.7875
84 D5M 0.414894 0.883117
85 AGO 0.414634 0.86747
86 ZGP 0.413223 0.848837
87 G1G 0.412698 0.857143
88 DBG 0.410853 0.878049
89 GPC 0.408 0.816092
90 MGD 0.408 0.827586
91 PGD 0.40625 0.857143
92 YYY 0.40625 0.848101
93 IDP 0.405941 0.897436
94 6OG 0.40404 0.875
95 DT DA DC DG 0.403974 0.860465
96 G U 0.401639 0.833333
97 DC DG DT DA 0.401316 0.860465
98 TPG 0.4 0.782609
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EM1; Ligand: TYD; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 3em1.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4M37 SAH None
2 2QES ADE 2.05479
3 3KU0 ADE 8.90411
4 1T0S BML 17.1233
5 4WB7 ATP 20
Pocket No.: 2; Query (leader) PDB : 3EM1; Ligand: TYD; 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: 3em1.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3EM1; Ligand: TYD; 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: 3em1.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3EM1; Ligand: TYD; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 3em1.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 6A1G 9OL 3.42466
2 5JWC FAD 5.47945
3 4NYT PC 9.58904
Pocket No.: 5; Query (leader) PDB : 3EM1; Ligand: TYD; 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: 3em1.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3EM1; Ligand: TYD; 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: 3em1.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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