Receptor
PDB id Resolution Class Description Source Keywords
3EE3 2.4 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF ACANTHAMOEBA POLYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH CDP ACANTHAMOEBA POLYPHAGA MIMIVIRUS PHOSPHOTRANSFERASE ATP-BINDING MIMIVIRUS 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
CDP A:160;
C:162;
D:163;
E:164;
F:165;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
CDP MG B:161;
Valid;
none;
submit data
424.458 n/a P(=O)...
MG A:161;
C:163;
D:164;
E:165;
F:166;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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: CDP; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 HF4 0.895522 1
3 CTP 0.895522 1
4 CAR 0.787879 0.985507
5 C 0.787879 0.985507
6 C5P 0.787879 0.985507
7 7XL 0.77027 0.944444
8 0RC 0.77027 0.918919
9 2TM 0.743243 0.958333
10 C2G 0.74026 0.957747
11 CDC 0.725 0.82716
12 CDP MG 0.722222 0.942857
13 C5G 0.707317 0.944444
14 CDM 0.695122 0.894737
15 CXY 0.678571 0.944444
16 AR3 0.636364 0.857143
17 CTN 0.636364 0.857143
18 1AA 0.619565 0.906667
19 A7R 0.606383 0.931507
20 UDP 0.605263 0.942029
21 I5A 0.602941 0.816901
22 YYY 0.582278 0.90411
23 CDP RB0 0.577778 0.917808
24 GCQ 0.560976 0.90411
25 C3P 0.56 0.942857
26 MCN 0.557692 0.819277
27 PMT 0.554455 0.85
28 91P 0.553398 0.851852
29 UTP 0.54321 0.942029
30 2AA 0.542857 0.693878
31 16B 0.538462 0.917808
32 CSV 0.536842 0.905405
33 CSQ 0.536842 0.905405
34 U5F 0.536585 0.942029
35 DCP 0.535714 0.90411
36 GTF 0.523256 0.90411
37 C2P 0.519481 0.957143
38 PCD 0.517857 0.781609
39 FZQ 0.511364 0.797619
40 FN5 0.509434 0.871795
41 GPC 0.509091 0.819277
42 CSF 0.504587 0.871795
43 DKZ 0.5 0.746667
44 NCC 0.495413 0.918919
45 HQ5 0.48913 0.758621
46 UNP 0.488372 0.915493
47 DCT 0.488372 0.90411
48 TKW 0.4875 0.971429
49 G G 6MZ C 0.486239 0.814815
50 G C 0.481818 0.8375
51 5GW 0.477778 0.890411
52 5HM 0.47561 0.958333
53 BUP 0.471264 0.878378
54 YSC 0.469388 0.767442
55 DCM 0.463415 0.890411
56 DC 0.463415 0.890411
57 UPP 0.451613 0.888889
58 UDH 0.451613 0.844156
59 G8D 0.450549 0.907895
60 U 0.45 0.927536
61 U5P 0.45 0.927536
62 C5P SIA 0.447368 0.893333
63 660 0.446809 0.876712
64 UFM 0.446809 0.888889
65 GDU 0.446809 0.888889
66 URM 0.446809 0.876712
67 UPG 0.446809 0.888889
68 8OD 0.445652 0.855263
69 0KX 0.444444 0.88
70 UPU 0.444444 0.887324
71 4GW 0.443299 0.866667
72 DOC 0.439024 0.890411
73 M7G 0.43617 0.829268
74 U2F 0.43299 0.842105
75 UFG 0.43299 0.842105
76 UPF 0.43299 0.842105
77 2KH 0.431818 0.915493
78 AWU 0.427083 0.888889
79 CG2 0.421053 0.873418
80 G3N 0.42 0.890411
81 UDP UDP 0.418605 0.885714
82 UDX 0.418367 0.888889
83 UAD 0.418367 0.888889
84 44P 0.416667 0.902778
85 3UC 0.415842 0.842105
86 DCP MG 0.413043 0.851351
87 M7M 0.412371 0.797619
88 8GT 0.410526 0.907895
89 V12 0.41 0.75
90 UGB 0.41 0.901408
91 UGA 0.41 0.901408
92 USQ 0.41 0.780488
93 UGF 0.405941 0.853333
94 UP5 0.405405 0.857143
95 GEO 0.405063 0.783784
96 UDM 0.403846 0.864865
97 H6Y 0.402062 0.855263
98 NVG 0.401961 0.731707
99 CTP C C C C 0.4 0.915493
100 6MZ C U 0.4 0.814815
Ligand no: 2; Ligand: CDP MG; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP MG 1 1
2 CAR 0.735294 0.956522
3 C 0.735294 0.956522
4 C5P 0.735294 0.956522
5 CDP 0.722222 0.942857
6 CDP RB0 0.690476 0.943662
7 CTP 0.671053 0.942857
8 HF4 0.671053 0.942857
9 CDC 0.662651 0.848101
10 2TM 0.653846 0.90411
11 7XL 0.6375 0.916667
12 0RC 0.6375 0.891892
13 C2G 0.614458 0.929577
14 UDP UDP 0.605263 0.940298
15 AR3 0.588235 0.855072
16 CTN 0.588235 0.855072
17 CXY 0.58427 0.916667
18 I5A 0.57971 0.84058
19 CDM 0.579545 0.868421
20 C5G 0.573034 0.916667
21 G G 6MZ C 0.528302 0.858974
22 G C 0.523364 0.858974
23 1AA 0.520408 0.88
24 DCP MG 0.511628 0.901408
25 FZQ 0.511364 0.77381
26 A7R 0.51 0.930556
27 CSQ 0.505155 0.90411
28 CSV 0.505155 0.90411
29 C3P 0.5 0.914286
30 C5P SIA 0.5 0.917808
31 16B 0.5 0.890411
32 CTP C C C C 0.495146 0.942029
33 HQ5 0.48913 0.755814
34 MCN 0.486239 0.795181
35 FN5 0.481481 0.846154
36 91P 0.481481 0.82716
37 PMT 0.481132 0.825
38 YSC 0.469388 0.764706
39 C2P 0.4625 0.901408
40 DKZ 0.461538 0.743243
41 2AA 0.459459 0.673469
42 NCC 0.442478 0.891892
43 CSF 0.438596 0.846154
44 TKW 0.433735 0.942857
45 6MZ C U 0.433071 0.858974
46 UDP GAL 0.43299 0.887324
47 GPC 0.431034 0.795181
48 PCD 0.428571 0.758621
49 5HM 0.423529 0.90411
50 DOC 0.421687 0.863014
51 YYY 0.420455 0.851351
52 UDP 0.418605 0.885714
53 G 6MZ C U 0.415385 0.87013
54 U 0.414634 0.898551
55 U5P 0.414634 0.898551
56 DCM 0.411765 0.863014
57 DC 0.411765 0.863014
58 V12 0.41 0.746835
59 GCQ 0.406593 0.851351
60 DCP 0.402174 0.851351
61 NVG 0.401961 0.728395
62 OMC OMU OMG OMG U 0.401515 0.82716
63 44P 0.4 0.849315
Similar Ligands (3D)
Ligand no: 1; Ligand: CDP; Similar ligands found: 38
No: Ligand Similarity coefficient
1 DUD 0.9790
2 TBD 0.9634
3 TYD 0.9611
4 ADP 0.9333
5 D4D 0.9313
6 DUN 0.9274
7 ADX 0.9253
8 IDP 0.9252
9 BEF ADP 0.9235
10 AU1 0.9225
11 AN2 0.9215
12 ADP MG 0.9194
13 UMP 0.9193
14 AP2 0.9182
15 A12 0.9182
16 DGI 0.9158
17 M33 0.9122
18 CUU 0.9102
19 GDP 0.9093
20 AMP 0.9080
21 U3S 0.9071
22 DAT 0.9016
23 TMP 0.8942
24 U1S 0.8914
25 CH 0.8874
26 H2U 0.8816
27 2A5 0.8762
28 DU 0.8746
29 SON 0.8726
30 SSA 0.8707
31 AZD 0.8684
32 7D3 0.8672
33 T3S 0.8656
34 DDN 0.8643
35 DUT 0.8631
36 AMZ 0.8619
37 C8M 0.8613
38 BMP 0.8569
Ligand no: 2; Ligand: CDP MG; Similar ligands found: 9
No: Ligand Similarity coefficient
1 DUD 0.9540
2 TYD 0.9413
3 TBD 0.9375
4 ADP 0.9246
5 IDP 0.8939
6 GDP 0.8931
7 D4D 0.8865
8 DGI 0.8830
9 UTP 0.8720
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
APoc FAQ
Feedback