Receptor
PDB id Resolution Class Description Source Keywords
4LP0 1.95 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF A TOPOISOMERASE ATP INHIBITOR STREPTOCOCCUS PNEUMONIAE PROTEIN-INHIBITOR COMPLEX ATP BINDING STRUCTURE-BASED DRUGANTIMICROBIAL VIRTUAL SCREEN ATPASE DOMAIN ISOMERASE-ISOINHIBITOR COMPLEX
Ref.: FRAGMENT-TO-HIT-TO-LEAD DISCOVERY OF A NOVEL PYRIDY SCAFFOLD OF ATP COMPETITIVE DUAL TARGETING TYPE II TOPOISOMERASE INHIBITING ANTIBACTERIAL AGENTS. J.MED.CHEM. V. 56 8712 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1YM A:301;
Valid;
none;
ic50 < 10 nM
437.396 C18 H14 F3 N5 O3 S CCNC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4EMV 1.7 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF A TOPOISOMERASE ATP INHIBITOR STREPTOCOCCUS PNEUMONIAE GA47373 PROTEIN-INHIBITOR COMPLEX ATP BINDING STRUCTURE-BASED DRUGANTIMICROBIAL VIRTUAL SCREEN ISOMERASE-ISOMERASE INHIBITO
Ref.: DISCOVERY OF A NOVEL AZAINDOLE CLASS OF ANTIBACTERI TARGETING THE ATPASE DOMAINS OF DNA GYRASE AND TOPO IV. BIOORG.MED.CHEM.LETT. V. 22 5150 2012
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
2 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
3 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
4 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
5 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
6 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
7 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
2 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
3 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
4 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
5 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
6 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
7 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
8 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
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: 1YM; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 1YM 1 1
2 1YP 0.652632 0.830986
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EMV; Ligand: 0R9; Similar sites found: 54
This union binding pocket(no: 1) in the query (biounit: 4emv.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TDF FAD 0.02126 0.40937 1.76991
2 1QY8 RDI 0.00003654 0.50966 2.21239
3 4XMF HSM 0.01012 0.43207 2.71739
4 5IXG OTP 0.00512 0.43716 2.95858
5 4WOE ADP 0.004073 0.4438 3.09735
6 4OYA 1VE 0.02814 0.41243 3.53982
7 2RCU BUJ 0.02336 0.41114 3.53982
8 5KBE IPH 0.01847 0.40728 3.53982
9 5H2U 1N1 0.007493 0.40589 3.53982
10 5IDM ANP 0.0001628 0.4639 3.91061
11 2GFD RDA 0.000111 0.48625 3.9823
12 5Y3N 8MF 0.0008401 0.46379 3.9823
13 1HSR BHO 0.03139 0.40007 3.9823
14 1I58 ADP 0.0005302 0.4316 4.2328
15 1I58 ACP 0.001774 0.42974 4.2328
16 4IVG ANP 0.0099 0.4005 4.86726
17 4XCL AGS 0.0003353 0.44927 5.30973
18 4GCZ ADP 0.002303 0.4161 5.30973
19 5MRH Q9Z 0.01457 0.40811 5.75221
20 5DQ8 FLF 0.01352 0.4028 5.83333
21 3L9R L9R 0.01523 0.40396 6.12245
22 1TID ATP 0.003795 0.40766 6.61765
23 1LSH PLD 0.005078 0.42074 6.63717
24 2IOR ADP 0.000919 0.40612 7.07965
25 1GKZ ADP 0.0006263 0.4452 7.52212
26 3CTL S6P 0.005841 0.40542 7.9646
27 1RYD GLC 0.001822 0.46431 8.40708
28 1NJR XYL 0.006176 0.41554 8.40708
29 3CV2 COA 0.008402 0.4189 8.84956
30 1BGQ RDC 0.0002145 0.47922 8.88889
31 5F5R ANP 0.0008296 0.46977 9.29204
32 5D3X 4IP 0.01911 0.40576 9.58084
33 2O1V ADP 0.0002669 0.4306 9.73451
34 2RKV ZBA 0.01375 0.40925 10.177
35 3WV6 GAL BGC 0.01167 0.42658 10.6195
36 3WV6 GAL GLC 0.01304 0.41135 10.6195
37 1KGI T4A 0.002012 0.43097 11.0236
38 3H4L ANP 0.0006164 0.4497 11.5044
39 2ZKJ ADP 0.0003196 0.48735 12.3894
40 3K60 ADP 0.0008422 0.40064 12.5561
41 2C2A ADP 0.0007567 0.43626 12.8319
42 1B63 ANP 0.001134 0.41506 13.2743
43 3D36 ADP 0.004113 0.41009 13.2743
44 1ID0 ANP 0.002017 0.40533 13.8158
45 1YC4 43P 0.00004686 0.46733 15.0442
46 5L2J 6UL 0.04936 0.40084 15.3061
47 4B7P 9UN 0.0001395 0.51121 15.9292
48 4RYV ZEA 0.004212 0.43002 16.129
49 3NMQ 7PP 0.001957 0.43649 16.3717
50 4XIZ LPP 0.007738 0.41629 17.1429
51 1TH8 ADP 0.0003788 0.42614 17.931
52 1Y8O ADP 0.0004026 0.42282 20.354
53 2XCM ADP 0.0003132 0.43942 20.6522
54 3A0T ADP 0.00546 0.4048 38.1579
Feedback