Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:142;
B:142;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
TYD A:143;
B:143;
Valid;
Valid;
none;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
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: TYD; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 TYD 1 1
2 TTP 0.884058 1
3 TMP 0.80597 0.985714
4 TLO 0.716049 0.945205
5 TTP MG 0.701299 0.943662
6 DAU 0.694118 0.932432
7 9RC 0.686747 0.829268
8 1JB 0.682353 0.932432
9 TRH 0.682353 0.932432
10 18T 0.682353 0.932432
11 3R2 0.682353 0.92
12 TDX 0.682353 0.945205
13 ATY 0.670886 0.945205
14 T3Q 0.666667 0.907895
15 DWN 0.666667 0.907895
16 3YN 0.666667 0.932432
17 T3F 0.666667 0.907895
18 TBD 0.662338 0.958904
19 T46 0.659091 0.932432
20 0N2 0.659091 0.896104
21 AZD 0.654321 0.907895
22 MMF 0.651685 0.907895
23 0FX 0.651685 0.907895
24 THM 0.641791 0.873239
25 LLT 0.641791 0.873239
26 QDM 0.637363 0.896104
27 JHZ 0.630435 0.884615
28 AKM 0.630435 0.886076
29 FNF 0.630435 0.92
30 1YF 0.630435 0.92
31 4TG 0.623656 0.92
32 DUD 0.61039 0.957143
33 0DN 0.6 0.833333
34 UFP 0.6 0.905405
35 QUH 0.58 0.907895
36 FUH 0.58 0.907895
37 T5A 0.572816 0.841463
38 BRU 0.571429 0.905405
39 5HU 0.571429 0.971831
40 FDM 0.564103 0.918919
41 5IU 0.564103 0.905405
42 NYM 0.564103 0.958333
43 T3P 0.56 0.943662
44 THP 0.556962 0.971429
45 ATM 0.542169 0.894737
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 3DR DT DT DT DT DT 0.540816 0.905405
49 TXS 0.538462 0.789474
50 YYY 0.536585 0.891892
51 T3S 0.525 0.789474
52 BVP 0.52381 0.944444
53 ABT 0.521739 0.884615
54 D4D 0.506024 0.928571
55 TQP 0.504274 0.864198
56 7SG 0.504274 0.864198
57 2DT 0.5 0.957747
58 T4K 0.5 0.853659
59 DT ME6 DT 0.5 0.87013
60 T5K 0.5 0.853659
61 TPE 0.5 0.894737
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 UMP 0.469136 0.942857
66 AZZ 0.469136 0.779221
67 DU 0.469136 0.942857
68 8GD 0.467391 0.829268
69 5CM 0.458824 0.918919
70 F6G 0.455556 0.855263
71 WMJ 0.452632 0.761905
72 D4T 0.449438 0.928571
73 DUP 0.449438 0.930556
74 6U4 0.447917 0.848101
75 ADS THS THS THS 0.444444 0.758621
76 DDN 0.439024 0.942857
77 3DT 0.428571 0.835616
78 UC5 0.425287 0.943662
79 ID2 0.423077 0.8
80 DT MA7 DT 0.420635 0.797619
81 8DG 0.418367 0.829268
82 DUT MG 0.417582 0.901408
83 DUN 0.41573 0.930556
84 O5W 0.411765 0.821429
85 5GW 0.410526 0.878378
86 DCM 0.406977 0.878378
87 DC 0.406977 0.878378
88 BUP 0.402174 0.842105
89 74X 0.4 0.732558
90 D4M 0.4 0.914286
91 74W 0.4 0.732558
Similar Ligands (3D)
Ligand no: 1; Ligand: TYD; Similar ligands found: 40
No: Ligand Similarity coefficient
1 UDP 0.9699
2 CDP 0.9611
3 GDP 0.9414
4 CDP MG 0.9413
5 ADP 0.9340
6 DAT 0.9300
7 DGI 0.9247
8 UDP UDP 0.9200
9 ADX 0.9182
10 ADP MG 0.9170
11 M33 0.9169
12 IDP 0.9166
13 AN2 0.9163
14 CA0 0.9151
15 GNH 0.9138
16 CUU 0.9101
17 AP2 0.9086
18 A12 0.9086
19 GCQ 0.9079
20 0RC 0.9061
21 M7G 0.9023
22 G8D 0.9005
23 QBT 0.8918
24 FZQ 0.8779
25 7XL 0.8744
26 DCP MG 0.8710
27 UTP 0.8698
28 C 0.8676
29 CTP 0.8658
30 C5P 0.8626
31 U5P 0.8621
32 AMP 0.8615
33 CAR 0.8608
34 523 0.8608
35 UP6 0.8582
36 9L3 0.8571
37 2KH 0.8564
38 H2U 0.8554
39 DOC 0.8546
40 FN5 0.8545
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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