Receptor
PDB id Resolution Class Description Source Keywords
5D7D 1.6 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
MPD B:302;
A:302;
B:303;
A:301;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
118.174 C6 H14 O2 C[C@@...
CL B:304;
A:303;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
MG A:305;
A:300;
A:304;
A:306;
B:307;
B:306;
B:305;
 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;
 submit data
24.305 Mg [Mg+2...
57X A:307;
B:308;
 Valid;
Valid;
 none;
none;
 submit data
337.399 C17 H15 N5 O S CCCN1...
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: 57X; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 57X 1 1
2 55H 0.4 0.71875
Similar Ligands (3D)
Ligand no: 1; Ligand: 57X; Similar ligands found: 26
No: Ligand Similarity coefficient
1 57Y 0.9128
2 C9G 0.9101
3 C9J 0.9056
4 BCE 0.8899
5 E0R 0.8898
6 9B2 0.8838
7 FJR 0.8816
8 F33 0.8802
9 97Z 0.8801
10 9AW 0.8799
11 9PC 0.8780
12 FKR 0.8773
13 RQ4 0.8773
14 675 0.8749
15 MD7 0.8737
16 IYX 0.8728
17 2ZT 0.8726
18 Y0R 0.8685
19 JV8 0.8683
20 W2E 0.8651
21 M0V 0.8646
22 M16 0.8639
23 1VG 0.8629
24 3TH 0.8575
25 J2Q 0.8531
26 EQN 0.8515
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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