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Receptor
PDB id Resolution Class Description Source Keywords
4EM7 1.9 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0RA A:301;
Valid;
none;
ic50 = 7.7 uM
266.295 C16 H14 N2 O2 c1cc(...
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 (50)
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 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
6 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
7 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
8 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
9 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
10 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
11 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
12 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
13 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PU9 - ADP BEF n/a n/a
18 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
22 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
23 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
24 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
25 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
26 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
27 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
28 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
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 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
34 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
35 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
36 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
37 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
38 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
39 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
40 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
41 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
42 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
43 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
44 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
45 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
46 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
47 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
48 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
49 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
50 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 0RA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 0RA 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EMV; Ligand: 0R9; Similar sites found with APoc: 127
This union binding pocket(no: 1) in the query (biounit: 4emv.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5HP8 PYR None
2 5OWC AYZ None
3 1F9V ADP 1.32743
4 1TDF FAD 1.76991
5 3SAO DBH 1.875
6 3KP6 SAL 1.98676
7 6D28 NEC 2.21239
8 3IHB GLU 2.21239
9 1ZX5 LFR 2.21239
10 5OF1 SAL 2.38095
11 1YP1 LYS ASN LEU 2.47525
12 3AQT RCO 2.65487
13 2F7A CCU 2.65487
14 3CEV ARG 2.65487
15 4DNJ ANN 2.65487
16 4XMF HSM 2.71739
17 5IXG OTP 2.95858
18 4WOE ADP 3.09735
19 1MJT ITU 3.09735
20 5YJS SAL 3.09735
21 3B6C SDN 3.09735
22 1QKQ MAN 3.52113
23 5IM3 DTP 3.53982
24 2PNC CLU 3.53982
25 4OYA 1VE 3.53982
26 2RCU BUJ 3.53982
27 5KBE IPH 3.53982
28 5H2U 1N1 3.53982
29 3JU6 ANP 3.53982
30 4X3R 686 3.53982
31 2GTF P1R 3.88889
32 5IDM ANP 3.91061
33 2GFD RDA 3.9823
34 5LX9 OLB 3.9823
35 5FPE 3TR 3.9823
36 5Y3N 8MF 3.9823
37 5X20 AOT 3.9823
38 1HSR BHO 3.9823
39 1I58 ADP 4.2328
40 1I58 ACP 4.2328
41 3NV3 GAL NAG MAN 4.34783
42 4RF7 ARG 4.42478
43 2G30 ALA ALA PHE 4.42478
44 2Z3U CRR 4.42478
45 3CBC DBS 4.54545
46 4LHD GLY 4.86726
47 4LED XXR 4.86726
48 2ZL7 FUC GAL NGA 4.86726
49 4IPE ANP 4.86726
50 4IVG ANP 4.86726
51 6GMN F4E 4.93827
52 1MFI FHC 5.26316
53 4XCL AGS 5.30973
54 4GCZ ADP 5.30973
55 4UBS DIF 5.75221
56 6AM8 TRP 5.75221
57 5MRH Q9Z 5.75221
58 1ELI PYC 5.75221
59 5DQ8 FLF 5.83333
60 4LBP 1WG 6
61 3L9R L9R 6.12245
62 5OKL PAM 6.19469
63 1TID ATP 6.61765
64 5G48 1FL 6.63717
65 1LSH PLD 6.63717
66 5AOG IAC 6.63717
67 5NM7 GLY 6.63717
68 5DYO FLU 6.88073
69 4GNC ASO 7.07965
70 4YRI 4JH 7.07965
71 2IOR ADP 7.07965
72 1GKZ ADP 7.52212
73 4DO1 ANN 7.52212
74 2ITM XUL 7.52212
75 3CTL S6P 7.9646
76 5KJW 53C 7.9646
77 6GNO XDI 8.14815
78 1KJ1 MAN 8.25688
79 1RYD GLC 8.40708
80 1NJR XYL 8.40708
81 5OF9 ANP 8.40708
82 3CV2 COA 8.84956
83 1BGQ RDC 8.88889
84 5OCG 9R5 8.99471
85 6FA4 D1W 9.24856
86 5F5R ANP 9.29204
87 5OLK DTP 9.29204
88 1ZEI CRS 9.43396
89 4OGQ 7PH 9.49721
90 5D3X 4IP 9.58084
91 2O1V ADP 9.73451
92 2AGC DAO 9.87654
93 4BIX ADP 10.177
94 2RKV ZBA 10.177
95 3WV6 GAL BGC 10.6195
96 3WV6 GAL GLC 10.6195
97 2VDF OCT 10.6195
98 5HWV MBN 10.7692
99 1KGI T4A 11.0236
100 3H4L ANP 11.5044
101 2YLD CMO 11.811
102 6H39 FGY 12.2449
103 2ZKJ ADP 12.3894
104 3K60 ADP 12.5561
105 2C2A ADP 12.8319
106 1B63 ANP 13.2743
107 3D36 ADP 13.2743
108 1I1Q TRP 13.7168
109 4ZDM GLY 13.7168
110 1ID0 ANP 13.8158
111 3KO0 TFP 13.8614
112 3BJE URA 14.1593
113 1YC4 43P 15.0442
114 5WL1 CUY 15.1515
115 5WL1 D3D 15.1515
116 4B7P 9UN 15.9292
117 4RYV ZEA 16.129
118 6G47 SIA SIA 16.2679
119 5J6A P46 16.3717
120 2YI0 YI0 16.8142
121 5UC4 83S 16.8182
122 4XIZ LPP 17.1429
123 1TH8 ADP 17.931
124 3DZ6 PUT 19.403
125 1Y8O ADP 20.354
126 2XCM ADP 20.6522
127 1PWB GLC 25.4237
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