Receptor
PDB id Resolution Class Description Source Keywords
5D7R 1.55 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYR COMPLEXED WITH A LIGAND STAPHYLOCOCCUS AUREUS DNA GYRASE GYRB LIGAND STRUCTURE-BASED DESIGN ISOMERASE-INHIBITOR COMPLEX
Ref.: DISCOVERY OF INDAZOLE DERIVATIVES AS A NOVEL CLASS BACTERIAL GYRASE B INHIBITORS. ACS MED.CHEM.LETT. V. 6 1080 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
57Y A:306;
B:307;
 Valid;
Valid;
 none;
none;
 ic50 = 0.013 uM
396.42 C19 H16 N4 O4 S CCCc1...
MG B:302;
B:304;
B:303;
A:302;
B:301;
A:304;
A:303;
A:301;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
MPD B:305;
 Invalid;
 none;
 submit data
118.174 C6 H14 O2 C[C@@...
CL B:306;
A:305;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TTZ 1.63 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF A TOPOISOMERASE ATPASE INHIBITOR STAPHYLOCOCCUS AUREUS PROTEIN-INHIBITOR COMPLEX ATP-BINDING STRUCTURE-BASED DRUGANTIMICROBIAL ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: PYRROLAMIDE DNA GYRASE INHIBITORS: OPTIMIZATION OF ANTIBACTERIAL ACTIVITY AND EFFICACY. BIOORG.MED.CHEM.LETT. V. 21 7416 2011
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
5 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
6 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
7 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
8 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
9 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
10 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
11 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
12 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
13 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
14 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
15 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
5 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
6 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
7 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
8 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
9 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
10 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
11 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
12 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
13 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
14 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
15 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
16 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
17 6Y8N ic50 = 9 nM OGH C21 H21 F N8 O Cc1ncc(cn1....
18 6Y8L - NOV C31 H36 N2 O11 Cc1c(ccc2c....
19 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
20 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 6KZV ic50 = 5.4 uM E0F C24 H27 N3 O2 CN(Cc1cccc....
5 6Y8O - NOV C31 H36 N2 O11 Cc1c(ccc2c....
6 4GEE Ki < 1 nM 0WT C17 H18 Cl N7 O CCc1c(c2c(....
7 4GGL Ki < 1 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
8 4HZ0 - 1AV C13 H9 N7 S c1cc(cnc1)....
9 1S14 - NOV C31 H36 N2 O11 Cc1c(ccc2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 57Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 57Y 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 57Y; Similar ligands found: 6
No: Ligand Similarity coefficient
1 57X 0.9128
2 C9J 0.9043
3 C9G 0.8867
4 FKR 0.8773
5 E0R 0.8749
6 9OJ 0.8682
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TTZ; Ligand: 07N; 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: 3ttz.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3TTZ; Ligand: 07N; 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: 3ttz.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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