Receptor
PDB id Resolution Class Description Source Keywords
4GFD 1.8 Å EC: 2.7.4.9 THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-6 STAPHYLOCOCCUS AUREUS SUBSP. AUREUS KINASE THYMIDINE MONPHOSPHATE SOLUBLE TRANSFERASE-TRANSFEINHIBITOR COMPLEX
Ref.: IN VIVO VALIDATION OF THYMIDYLATE KINASE (TMK) WITH RATIONALLY DESIGNED, SELECTIVE ANTIBACTERIAL COMPOU ACS CHEM.BIOL. V. 7 1866 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0YB A:301;
B:301;
Valid;
Valid;
none;
none;
Ki = 330 pM
584.501 C29 H34 Br N3 O5 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GFD 1.8 Å EC: 2.7.4.9 THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-6 STAPHYLOCOCCUS AUREUS SUBSP. AUREUS KINASE THYMIDINE MONPHOSPHATE SOLUBLE TRANSFERASE-TRANSFEINHIBITOR COMPLEX
Ref.: IN VIVO VALIDATION OF THYMIDYLATE KINASE (TMK) WITH RATIONALLY DESIGNED, SELECTIVE ANTIBACTERIAL COMPOU ACS CHEM.BIOL. V. 7 1866 2012
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4QGA ic50 = 12 nM 31Z C24 H23 Cl F N3 O5 CC1=CN(C(=....
2 4HLD ic50 = 0.5 nM 16T C22 H22 Cl N3 O6 S CC1=CN(C(=....
3 4QGG ic50 = 1 nM 32C C28 H31 Cl F N3 O5 CC1=CN(C(=....
4 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
5 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
6 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
7 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
8 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
9 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
11 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
12 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
13 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4QGA ic50 = 12 nM 31Z C24 H23 Cl F N3 O5 CC1=CN(C(=....
2 4HLD ic50 = 0.5 nM 16T C22 H22 Cl N3 O6 S CC1=CN(C(=....
3 4QGG ic50 = 1 nM 32C C28 H31 Cl F N3 O5 CC1=CN(C(=....
4 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
5 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
6 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
7 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
8 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
9 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
11 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
12 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
13 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
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: 0YB; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 0YB 1 1
2 13Y 0.666667 0.934211
3 32B 0.531746 0.8625
4 32C 0.519685 0.922078
5 32E 0.519685 0.922078
6 0Y5 0.484127 0.894737
7 T05 0.468254 0.725275
8 31Z 0.427481 0.883117
9 32K 0.427481 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GFD; Ligand: 0YB; 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: 4gfd.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4GFD; Ligand: 0YB; 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: 4gfd.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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