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Receptor
PDB id Resolution Class Description Source Keywords
2V54 2.4 Å EC: 2.7.4.9 CRYSTAL STRUCTURE OF VACCINIA VIRUS THYMIDYLATE KINASE BOUND TO TDP VACCINIA VIRUS COPENHAGEN NUCLEOTIDE BIOSYNTHESIS ATP-BINDING NUCLEOTIDE-BINDING KINASE POXVIRUS TMP KINASE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF POXVIRUS THYMIDYLATE KINASE: AN UNEXPECTED DIMERIZATION HAS IMPLICATIONS FOR ANTIVIRAL THERAPY PROC.NAT.ACAD.SCI.USA V. 105 16900 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:1205;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
POP B:1206;
Invalid;
none;
submit data
175.959 H2 O7 P2 O[P@@...
TYD A:1205;
B:1207;
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
2V54 2.4 Å EC: 2.7.4.9 CRYSTAL STRUCTURE OF VACCINIA VIRUS THYMIDYLATE KINASE BOUND TO TDP VACCINIA VIRUS COPENHAGEN NUCLEOTIDE BIOSYNTHESIS ATP-BINDING NUCLEOTIDE-BINDING KINASE POXVIRUS TMP KINASE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF POXVIRUS THYMIDYLATE KINASE: AN UNEXPECTED DIMERIZATION HAS IMPLICATIONS FOR ANTIVIRAL THERAPY PROC.NAT.ACAD.SCI.USA V. 105 16900 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2V54 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2V54 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
50% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2YOH Ki = 11 uM WMJ C17 H19 N5 O7 CC1=CN(C(=....
2 2YOF Ki = 25 uM 74W C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
3 2WWF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2YOG Ki = 31 uM 74X C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
5 2V54 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
6 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
7 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
8 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
9 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
10 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
11 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
12 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
13 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
14 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
15 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
16 4TMK Kd = 20 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
17 1E2Q - TMP C10 H15 N2 O8 P CC1=CN(C(=....
18 1E9C - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 1NN0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 1E2G - TMP C10 H15 N2 O8 P CC1=CN(C(=....
21 1NN1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
22 1NMX - FDM C10 H14 F N2 O7 P CC1=CN(C(=....
23 1E2E - AF3 Al F3 F[Al](F)F
24 1NN5 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 1E9B - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
26 1E2D - TMP C10 H15 N2 O8 P CC1=CN(C(=....
27 1E99 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
28 1NMY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 2XX3 - TAE C9 H14 N2 O8 P2 CC1=CN(C(=....
30 1NMZ - NYM C10 H16 N3 O7 P CC1=CN(C(=....
31 1E9D - ATM C10 H14 N5 O7 P CC1=CN(C(=....
32 1NN3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 1E9A - Z5A C20 H24 N10 O22 P5 CC1=CN(C(=....
34 1E9F - TMP C10 H15 N2 O8 P CC1=CN(C(=....
35 1E9E - TMP C10 H15 N2 O8 P CC1=CN(C(=....
36 1E98 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
37 1E2F - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
38 2TMK - ATM C10 H14 N5 O7 P CC1=CN(C(=....
39 3TMK Kd = 135 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
40 1TMK - TMP C10 H15 N2 O8 P CC1=CN(C(=....
41 5X8C - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
42 5ZB4 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
43 5ZAX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 5X86 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
45 5X8B - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 3UWO ic50 = 20 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
47 3UXM ic50 = 17 uM 0DN C10 H13 F N2 O4 CC1=CN(C(=....
48 5UIV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 5XB2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50 5XB3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
51 5XAI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
52 5H56 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
53 5H5B - FLC C6 H5 O7 C(C(=O)[O-....
54 5H5K - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYD; Similar ligands found: 87
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 DAU 0.694118 0.932432
6 1JB 0.682353 0.932432
7 TRH 0.682353 0.932432
8 3R2 0.682353 0.92
9 18T 0.682353 0.932432
10 TDX 0.682353 0.945205
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3Q 0.666667 0.907895
15 T3F 0.666667 0.907895
16 TBD 0.662338 0.958904
17 T46 0.659091 0.932432
18 0N2 0.659091 0.896104
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 THM 0.641791 0.873239
23 LLT 0.641791 0.873239
24 QDM 0.637363 0.896104
25 JHZ 0.630435 0.884615
26 1YF 0.630435 0.92
27 AKM 0.630435 0.886076
28 FNF 0.630435 0.92
29 4TG 0.623656 0.92
30 DT DT DT 0.616279 0.917808
31 DUD 0.61039 0.957143
32 UFP 0.6 0.905405
33 0DN 0.6 0.833333
34 DT DT DT DT DT 0.582418 0.945205
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 DT DT PST 0.569892 0.87013
41 FDM 0.564103 0.918919
42 5IU 0.564103 0.905405
43 NYM 0.564103 0.958333
44 T3P 0.56 0.943662
45 THP 0.556962 0.971429
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 ATM 0.542169 0.894737
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 7SG 0.504274 0.864198
56 TQP 0.504274 0.864198
57 T5K 0.5 0.853659
58 2DT 0.5 0.957747
59 TPE 0.5 0.894737
60 T4K 0.5 0.853659
61 DT ME6 DT 0.5 0.87013
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 AZZ 0.469136 0.779221
66 DU 0.469136 0.942857
67 UMP 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 DUP 0.449438 0.930556
71 D4T 0.449438 0.928571
72 6U4 0.447917 0.848101
73 ADS THS THS THS 0.444444 0.758621
74 DDN 0.439024 0.942857
75 3DT 0.428571 0.835616
76 UC5 0.425287 0.943662
77 ID2 0.423077 0.8
78 DT MA7 DT 0.420635 0.797619
79 8DG 0.418367 0.829268
80 DUN 0.41573 0.930556
81 5GW 0.410526 0.878378
82 DCM 0.406977 0.878378
83 DC 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 74W 0.4 0.732558
86 74X 0.4 0.732558
87 D4M 0.4 0.914286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V54; Ligand: TYD; Similar sites found with APoc: 19
This union binding pocket(no: 1) in the query (biounit: 2v54.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5AK0 8V1 2.45098
2 1DDU CB3 2.45098
3 1NCE CB3 2.45098
4 3T3Z 9PL 3.92157
5 1PNF NDG NAG 3.92157
6 2OZ5 7XY 4.41176
7 4URS C2E 4.78723
8 1P72 ADP 4.90196
9 1P72 THM 4.90196
10 1E2K TMC 6.37255
11 1KI6 AHU 6.37255
12 1M6P M6P 7.23684
13 2D24 XYS XYS 7.35294
14 5LLB 6YZ 7.84314
15 2Z48 A2G 8.82353
16 4S00 AKR 9.80392
17 2JAQ DCP 10.7843
18 2I5F 5IP 12.844
19 1OE0 TTP 33.3333
Pocket No.: 2; Query (leader) PDB : 2V54; Ligand: TYD; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 2v54.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5HR5 FLC 3.92157
2 1VL8 NAP 5.88235
3 5G41 AP5 7.84314
4 5LJ0 6XX 10.7692
5 3NV6 CAM 14.7059
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