Receptor
PDB id Resolution Class Description Source Keywords
4URL 2.29 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS NATURAL PRODUCT KIBDELOMYCIN GYRASTOPOISOMERASE IV
Ref.: STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. ACS CHEM.BIOL. V. 9 2023 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XAM B:2000;
A:2000;
Valid;
Valid;
none;
none;
ic50 = 500 nM
939.872 C44 H60 Cl2 N4 O14 Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4URL 2.29 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS NATURAL PRODUCT KIBDELOMYCIN GYRASTOPOISOMERASE IV
Ref.: STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. ACS CHEM.BIOL. V. 9 2023 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
50% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
2 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
3 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
4 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
5 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
6 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
7 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
8 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
9 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
10 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
11 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
12 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
15 4PU9 - ADP BEF n/a n/a
16 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
20 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
22 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
23 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
24 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
25 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
26 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
27 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
28 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
31 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
32 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
33 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
34 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
35 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XAM; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 XAM 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4URL; Ligand: XAM; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 4url.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GFD RDA 0.00007876 0.46041 2.9661
2 2O1V ADP 0.00007041 0.41514 3.20197
3 4IVG ANP 0.002001 0.40718 4.4335
4 1I58 ACP 0.0009686 0.40909 4.7619
5 1I58 ADP 0.0001655 0.40806 4.7619
6 1QY8 RDI 0.00002044 0.44801 4.92611
7 4XCL AGS 0.00009341 0.44326 5.01931
8 1BGQ RDC 0.000197 0.45556 5.77778
9 3H4L ANP 0.00008938 0.44939 5.99455
10 1Y8O ADP 0.00002386 0.42335 6.65025
11 2ZKJ ADP 0.0008681 0.445 7.1066
12 1B63 ANP 0.000568 0.42334 7.20721
13 4GCZ ADP 0.0004193 0.40838 7.88177
14 5L2J 6UL 0.02115 0.40379 8.16327
15 5L2J 70E 0.0225 0.40379 8.16327
16 2HKJ RDC 0.00002421 0.49363 8.86699
17 5IDM ANP 0.00002103 0.45351 9.49721
18 1GKZ ADP 0.0001777 0.42726 11.0825
19 2XCM ADP 0.00004539 0.43191 11.33
20 2C2A ADP 0.0001453 0.42495 12.0155
21 5F5R ANP 0.00009944 0.40381 13.0542
22 3EHG ATP 0.01077 0.41605 13.2812
23 1YC4 43P 0.000005308 0.4553 14.7727
24 4B7P 9UN 0.00004275 0.50699 16.9565
25 3D36 ADP 0.0002921 0.42308 22.1311
26 1TID ATP 0.0004271 0.4098 23.5294
27 1ZXM ANP 0.0001319 0.46248 31.5
28 1QZR ANP 0.0006632 0.43295 40.4306
29 1QZR CDX 0.005044 0.43213 40.4306
Pocket No.: 2; Query (leader) PDB : 4URL; Ligand: XAM; Similar sites found: 1
This union binding pocket(no: 2) in the query (biounit: 4url.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TH8 ADP 0.0001862 0.41329 18.6207
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