Receptor
PDB id Resolution Class Description Source Keywords
3ELH 2.4 Å EC: 2.7.4.6 X-RAY STRUCTURE OF ACANTHAMOEBA PLOYPHAGA MIMIVIRUS NUCLEOSI DIPHOSPHATE KINASE COMPLEXED WITH DUDP ACANTHAMOEBA POLYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE MIMIVIRUS PHOSPHOTRANSFERASE NBINDING ATP-BINDING KINASE MAGNESIUM METAL-BINDING NUCMETABOLISM NUCLEOTIDE-BINDING PHOSPHOPROTEIN TRANSFERASE
Ref.: DISSECTING THE UNIQUE NUCLEOTIDE SPECIFICITY OF MIM 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
DUD A:160;
B:161;
C:162;
D:163;
E:164;
F:165;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
 submit data
388.162 C9 H14 N2 O11 P2 C1[C@...
MG A:161;
B:162;
C:163;
D:164;
E:165;
F:166;
 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 11 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 (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: DUD; Similar ligands found: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 DUD 1 1
2 DUT 0.880597 1
3 UMP 0.8 0.985075
4 DU 0.8 0.985075
5 DUP 0.739726 0.971014
6 UC5 0.71831 0.985294
7 DUN 0.69863 0.971014
8 DUT MG 0.693333 0.941176
9 UMP AF3 PO4 0.653846 0.864865
10 DUS 0.642857 0.842105
11 DUR 0.630769 0.867647
12 TYD 0.61039 0.957143
13 YYY 0.589744 0.929577
14 UDP 0.571429 0.913043
15 TTP 0.542169 0.957143
16 UM3 0.540541 0.941176
17 DCP 0.52381 0.929577
18 DU DU DU DU BRU DU DU 0.52 0.853333
19 UTP 0.512195 0.913043
20 DDN 0.506494 0.985075
21 U5F 0.506024 0.913043
22 UFP 0.493671 0.916667
23 DDU 0.485714 0.742857
24 F6G 0.482759 0.890411
25 8GD 0.477778 0.8375
26 TMP 0.469136 0.942857
27 5HU 0.469136 0.957143
28 BRU 0.469136 0.916667
29 8DD 0.467391 0.844156
30 DU4 0.465909 0.75
31 5IU 0.463415 0.916667
32 DU3 0.45977 0.794521
33 UNP 0.45977 0.887324
34 DUA 0.45977 0.797297
35 6U4 0.457447 0.857143
36 DCM 0.451219 0.915493
37 DC 0.451219 0.915493
38 DAU 0.44898 0.891892
39 TLO 0.442105 0.90411
40 18T 0.438776 0.891892
41 TRH 0.438776 0.891892
42 1JB 0.438776 0.891892
43 U5P 0.4375 0.898551
44 U 0.4375 0.898551
45 UDX 0.4375 0.887324
46 UAD 0.4375 0.887324
47 0FX 0.435644 0.868421
48 0KX 0.433333 0.90411
49 BVP 0.431818 0.929577
50 T3Q 0.43 0.868421
51 T3F 0.43 0.868421
52 139 0.428571 0.8125
53 ATY 0.428571 0.90411
54 8DG 0.427083 0.8375
55 T46 0.425743 0.891892
56 UDH 0.425532 0.891892
57 3R2 0.424242 0.88
58 TDX 0.424242 0.90411
59 9RC 0.42268 0.792683
60 MMF 0.421569 0.868421
61 UPG 0.421053 0.861111
62 GDU 0.421053 0.861111
63 660 0.421053 0.901408
64 UFM 0.421053 0.861111
65 URM 0.421053 0.901408
66 2KH 0.420455 0.887324
67 AZD 0.419355 0.868421
68 UPU 0.417582 0.859155
69 TTP MG 0.417582 0.901408
70 DWN 0.415842 0.868421
71 3YN 0.415842 0.891892
72 DGI 0.414894 0.7875
73 UMC 0.414634 0.927536
74 QDM 0.413462 0.857143
75 0N2 0.411765 0.857143
76 UPP 0.410526 0.861111
77 FNF 0.409524 0.88
78 AKM 0.409524 0.848101
79 1YF 0.409524 0.88
80 PUP 0.408163 0.942029
81 UPF 0.408163 0.815789
82 U2F 0.408163 0.815789
83 UFG 0.408163 0.815789
84 UA3 0.407407 0.884058
85 U2P 0.407407 0.898551
86 U3P 0.407407 0.884058
87 UDP UDP 0.406977 0.857143
88 3UC 0.405941 0.815789
89 4TG 0.40566 0.88
90 44P 0.404762 0.928571
91 DUX 0.404494 0.746667
92 DCP MG 0.402174 0.875
93 AWU 0.402062 0.861111
94 PUA 0.4 0.846154
Similar Ligands (3D)
Ligand no: 1; Ligand: DUD; Similar ligands found: 22
No: Ligand Similarity coefficient
1 CDP 0.9790
2 TBD 0.9720
3 CDP MG 0.9540
4 D4D 0.9430
5 ADP 0.9233
6 DAT 0.9204
7 ADX 0.9092
8 GCQ 0.9091
9 GDP 0.8888
10 IDP 0.8882
11 7D3 0.8807
12 7XL 0.8739
13 C5P 0.8692
14 FZK 0.8683
15 D4T 0.8669
16 9KE 0.8635
17 CAR 0.8609
18 FZQ 0.8603
19 A12 0.8600
20 UP6 0.8597
21 NYM 0.8571
22 9KB 0.8543
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3em1.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3em1.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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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