Receptor
PDB id Resolution Class Description Source Keywords
4QGA 1.94 Å EC: 2.7.4.9 S.AUREUS TMK IN COMPLEX WITH POTENT INHIBITOR COMPOUND 19, 2 CHLOROPHENOXY)-3-FLUORO-4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-D IHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}BENZOIC ACI STAPHYLOCOCCUS AUREUS SUBSP. AUREUS TRANSFERASE/TRANSFERASE INHIBITOR KINASE THYMIDINE MONPHOSPTRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: ANTIBACTERIAL INHIBITORS OF GRAM-POSITIVE THYMIDYLA KINASE: STRUCTURE-ACTIVITY RELATIONSHIPS AND CHIRAL PREFERENCE OF A NEW HYDROPHOBIC BINDING REGION. J.MED.CHEM. V. 57 4584 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
31Z A:301;
B:301;
 Valid;
Valid;
 none;
none;
 ic50 = 12 nM
487.908 C24 H23 Cl F N3 O5 CC1=C...
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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 (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 5TMP Kd = 34 nM Z5A C20 H24 N10 O22 P5 CC1=CN(C(=....
5 5ZB0 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
6 3UWK ic50 = 58 uM 0DF C13 H11 N3 O CN1c2cc(cn....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 31Z; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 31Z 1 1
2 32K 0.75 0.932432
3 32C 0.634783 0.958904
4 32E 0.634783 0.958904
5 32B 0.566667 0.92
6 0Y5 0.555556 0.957747
7 13Y 0.528926 0.945205
8 14D 0.508929 0.901408
9 16T 0.459016 0.761364
10 T05 0.44 0.727273
11 0YB 0.427481 0.883117
12 YUI 0.416 0.902778
Similar Ligands (3D)
Ligand no: 1; Ligand: 31Z; Similar ligands found: 0
No: Ligand Similarity coefficient
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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