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 (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
13 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 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 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
13 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
14 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
15 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
50% Homology Family (15)
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 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 4GEE Ki < 1 nM 0WT C17 H18 Cl N7 O CCc1c(c2c(....
6 4GGL Ki < 1 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
7 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
8 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
9 4HZ0 - 1AV C13 H9 N7 S c1cc(cnc1)....
10 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
11 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
12 1S14 - NOV C31 H36 N2 O11 Cc1c(ccc2c....
13 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
14 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
15 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 57Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 57Y 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TTZ; Ligand: 07N; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 3ttz.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KO0 TFP 0.01584 0.40716 None
2 3CBC DBS 0.002099 0.45967 1.51515
3 2F6U CIT 0.01183 0.40899 1.51515
4 5H2U 1N1 0.002069 0.40805 1.51515
5 3EHH ADP 0.01418 0.40059 2.0202
6 2PNC CLU 0.001035 0.47107 2.52525
7 2G30 ALA ALA PHE 0.003746 0.42298 2.52525
8 3VPH FBP 0.009401 0.41753 2.52525
9 3AQT RCO 0.009186 0.41405 2.52525
10 3RF4 FUN 0.01076 0.41103 2.58621
11 4DSU BZI 0.0008538 0.47128 2.6455
12 5Y3N 8MF 0.003648 0.42422 3.0303
13 1QKQ MAN 0.0003714 0.49171 3.52113
14 2IOR ADP 0.00007106 0.51916 3.53535
15 5D9G GLU ASN LEU TYR PHE GLN 0.006659 0.4165 3.53535
16 5FUI APY 0.01356 0.43897 3.78788
17 3S5W ONH 0.009926 0.40674 4.0404
18 2ZL7 FUC GAL NGA 0.01392 0.4048 4.0404
19 5F6U 5VK 0.02049 0.40015 4.4586
20 1QY8 RDI 0.0002321 0.45584 4.54545
21 2O1V ADP 0.0007918 0.4554 4.54545
22 4BIX ADP 0.00724 0.4196 4.54545
23 5DYO FLU 0.01098 0.4128 4.54545
24 2GFD RDA 0.0003199 0.40665 4.54545
25 5F5R ANP 0.0002117 0.48877 5.05051
26 4KBA 1QM 0.01104 0.40588 5.05051
27 1YC4 43P 0.00009668 0.49183 5.55556
28 3K60 ADP 0.001637 0.45165 5.55556
29 3NMQ 7PP 0.00311 0.41515 5.55556
30 5KJW 53C 0.01442 0.40699 5.55556
31 4RYV ZEA 0.006499 0.41241 5.80645
32 3WXL ADP 0.004199 0.42082 6.06061
33 4XCL AGS 0.0004285 0.42161 6.56566
34 1YP1 LYS ASN LEU 0.0154 0.40327 6.56566
35 2BVE PH5 0.01564 0.40828 6.72269
36 3SAO DBH 0.002211 0.44963 6.875
37 4WOE ADP 0.001225 0.46071 7.07071
38 3JU6 ANP 0.006593 0.42162 7.07071
39 2GTF P1R 0.0002858 0.47956 7.77778
40 5HP8 PYR 0.01424 0.4149 8.06452
41 5IDM ANP 0.0004061 0.43475 8.93855
42 1ZNY GDP 0.004514 0.42979 11.6162
43 1GKZ ADP 0.0004002 0.425 11.6162
44 2UYN 2KT 0.02084 0.40501 11.6279
45 5FPE 3TR 0.01185 0.41563 13.1313
46 3H4L ANP 0.0005932 0.41025 13.1313
47 3QSB 743 0.008489 0.40694 13.6364
48 1BRW URA 0.0115 0.41086 14.6465
49 2TPI ILE VAL 0.002613 0.40361 15.5172
50 1ID0 ANP 0.002588 0.42644 15.7895
51 5HES 032 0.01667 0.40233 16.1616
52 3NZ1 3NY 0.008619 0.42185 17.1717
53 2P1M IHP 0.01929 0.4037 17.1717
54 2XCM ADP 0.0005931 0.44654 20.6522
55 1I58 ADP 0.0001405 0.47276 21.164
56 1I58 ACP 0.0007833 0.40184 21.164
57 1TID ATP 0.002156 0.40645 21.3235
58 3CV2 COA 0.01227 0.40262 22.2222
Pocket No.: 2; Query (leader) PDB : 3TTZ; Ligand: 07N; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 3ttz.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1I7M PUT 0.02086 0.40043 4.47761
2 2GBB CIT 0.01132 0.40758 5.12821
3 4FFG 0U8 0.01168 0.40888 7.07071
4 1Q19 SSC 0.01404 0.40368 9.09091
5 3WV6 GAL GLC 0.01764 0.40105 10.6061
6 2WZ5 MET 0.00249 0.44375 16.3399
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