Receptor
PDB id Resolution Class Description Source Keywords
3EVM 1.8 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF THE MIMIVIRUS NDK +KPN-N62L-R107G TRIPL COMPLEXED WITH DCDP ACANTHAMOEBA POLYPHAGA MIMIVIRUS PHOSPHOTRANSFERASE NUCLEOTIDE BINDING ATP-BINDING KINASE MAGNESIUM METAL-BINDING NUCLEOTIDE METABOLISM NUCLEOTIDEPHOSPHOPROTEIN 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
MG A:202;
B:202;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
YYY A:201;
B:201;
Valid;
Valid;
none;
none;
submit data
387.177 C9 H15 N3 O10 P2 C1[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: YYY; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 YYY 1 1
2 DCP 0.884058 1
3 DC 0.80597 0.985714
4 DCM 0.80597 0.985714
5 0KX 0.746667 0.972222
6 DCP MG 0.701299 0.943662
7 DCZ 0.641791 0.847222
8 LDC 0.641791 0.847222
9 DUD 0.589744 0.929577
10 CDP 0.582278 0.90411
11 GCQ 0.554217 0.891892
12 TYD 0.536585 0.891892
13 DCT 0.535714 0.971831
14 CTP 0.52381 0.90411
15 DUT 0.52381 0.929577
16 HF4 0.52381 0.90411
17 GTF 0.5 0.891892
18 5CM 0.493976 0.945205
19 DOC 0.4875 0.957747
20 CPA 0.485981 0.85
21 8GD 0.483516 0.875
22 6U4 0.478723 0.921053
23 TTP 0.477273 0.891892
24 CGP 0.468468 0.841463
25 0RC 0.466667 0.881579
26 7XL 0.466667 0.88
27 8DD 0.457447 0.835443
28 C 0.451219 0.890411
29 UMP 0.451219 0.915493
30 CAR 0.451219 0.890411
31 DU 0.451219 0.915493
32 C5P 0.451219 0.890411
33 CXY 0.44898 0.88
34 CDC 0.447917 0.77381
35 2TM 0.444444 0.918919
36 F6G 0.43956 0.905405
37 C2G 0.43617 0.891892
38 DUP 0.433333 0.90411
39 8DG 0.43299 0.875
40 CDM 0.428571 0.858974
41 C5G 0.424242 0.855263
42 DDN 0.421687 0.915493
43 C3P 0.421687 0.876712
44 C2P 0.421687 0.916667
45 CDP MG 0.420455 0.851351
46 UFP 0.411765 0.855263
47 LTT 0.410256 0.77027
48 UC5 0.409091 0.916667
49 DAT 0.408602 0.831169
50 TMP 0.406977 0.878378
51 BRU 0.406977 0.855263
52 DGI 0.40625 0.848101
53 3TC 0.405063 0.76
54 TLO 0.40404 0.844156
55 DUT MG 0.402174 0.875
56 DUN 0.4 0.90411
57 0FX 0.4 0.835443
Similar Ligands (3D)
Ligand no: 1; Ligand: YYY; Similar ligands found: 13
No: Ligand Similarity coefficient
1 TBD 0.9804
2 UDP 0.9739
3 D4D 0.9416
4 ADP 0.9230
5 GDP 0.9086
6 IDP 0.9078
7 UDP UDP 0.8950
8 ADX 0.8846
9 44P 0.8784
10 AZD 0.8779
11 SON 0.8695
12 UTP 0.8596
13 2KH 0.8540
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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