Receptor
PDB id Resolution Class Description Source Keywords
1KZN 2.3 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF E. COLI 24KDA DOMAIN IN COMPLEX WITH CLOROBIOCIN ESCHERICHIA COLI TOPOISOMERASE GYRASE B CLOROBIOCIN
Ref.: DNA GYRASE INTERACTION WITH COUMARIN-BASED INHIBITORS: THE ROLE OF THE HYDROXYBENZOATE ISOPENTENYL MOIETY AND THE 5'-METHYL GROUP OF THE NOVIOSE. BIOCHEMISTRY V. 41 7217 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CBN A:1;
Valid;
none;
Kd = 1.2 nM
697.128 C35 H37 Cl N2 O11 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KZN 2.3 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF E. COLI 24KDA DOMAIN IN COMPLEX WITH CLOROBIOCIN ESCHERICHIA COLI TOPOISOMERASE GYRASE B CLOROBIOCIN
Ref.: DNA GYRASE INTERACTION WITH COUMARIN-BASED INHIBITORS: THE ROLE OF THE HYDROXYBENZOATE ISOPENTENYL MOIETY AND THE 5'-METHYL GROUP OF THE NOVIOSE. BIOCHEMISTRY V. 41 7217 2002
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
2 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
3 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
4 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
5 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
6 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
2 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
3 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
4 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
5 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
6 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
7 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S 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: CBN; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 CBN 1 1
2 NOV 0.669291 0.820895
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KZN; Ligand: CBN; Similar sites found: 97
This union binding pocket(no: 1) in the query (biounit: 1kzn.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1M48 FRG 0.004464 0.43874 None
2 1UO4 PIH 0.03616 0.40118 None
3 1NF8 BOG 0.003061 0.45776 0.97561
4 1Q3A NGH 0.0168 0.40503 1.21212
5 1QY8 RDI 0.00001152 0.50503 1.95122
6 2GFD RDA 0.00003854 0.46474 1.95122
7 4JWK CTN 0.009333 0.4269 2.07254
8 1BGQ RDC 0.00003551 0.44671 2.43902
9 4F4P 0SB 0.02634 0.41066 2.43902
10 3JU6 ANP 0.01776 0.40816 2.43902
11 3CBC DBS 0.004281 0.45008 2.52525
12 1QKQ MAN 0.0009444 0.44935 2.8169
13 2O1V ADP 0.00006948 0.51594 2.92683
14 3O01 DXC 0.008128 0.4139 2.92683
15 3QSB 743 0.01377 0.40513 2.92683
16 3G5D 1N1 0.03243 0.40129 2.92683
17 1YP1 LYS ASN LEU 0.02082 0.40462 2.9703
18 3SAO DBH 0.008494 0.43008 3.125
19 4EKQ NPO 0.01104 0.40979 3.20856
20 4B7P 9UN 0.00004111 0.53632 3.41463
21 3K60 ADP 0.0001833 0.50917 3.41463
22 2PNC CLU 0.0141 0.41722 3.41463
23 5H2U 1N1 0.004221 0.41326 3.41463
24 3IHB GLU 0.02005 0.4031 3.50877
25 5DCH 1YO 0.009417 0.42443 3.64583
26 4DSU BZI 0.002794 0.45096 3.7037
27 1RL4 BRR 0.01757 0.4084 3.7234
28 4BIX ADP 0.001111 0.46944 3.90244
29 2VDF OCT 0.000625 0.45831 3.90244
30 2PYY GLU 0.01252 0.41139 3.90244
31 1C5C TK4 0.01725 0.41127 3.90244
32 1E4I NFG 0.008269 0.40538 3.90244
33 2F9W PAU 0.02119 0.4 3.90244
34 2WZ5 MET 0.009319 0.40878 3.92157
35 4K55 H6P 0.01298 0.40876 4.03226
36 2C2A ADP 0.0001 0.48459 4.39024
37 4XCL AGS 0.0001414 0.46508 4.39024
38 5F5R ANP 0.00007663 0.45177 4.39024
39 5Y3N 8MF 0.002398 0.44183 4.39024
40 4FFG 0U8 0.01225 0.42485 4.39024
41 2ZL7 FUC GAL NGA 0.01885 0.4069 4.39024
42 1RM8 BAT 0.01561 0.41103 4.73373
43 1BRW URA 0.007332 0.42956 4.87805
44 3QDV NDG 0.03027 0.40237 4.8951
45 1RYD GLC 0.002732 0.45138 4.90956
46 3KO0 TFP 0.005452 0.43838 4.9505
47 5IDM ANP 0.00001969 0.50246 5.02793
48 1MFI FHC 0.01187 0.42292 5.26316
49 4XIZ LPP 0.01379 0.4048 5.29412
50 4G4P GLN 0.01531 0.41146 5.32787
51 2IOR ADP 0.00001953 0.55853 5.36585
52 3AQT RCO 0.003716 0.44528 5.36585
53 5XDT ZI7 0.01081 0.40323 5.36585
54 4IN9 SER TRP PHE PRO 0.01409 0.41754 5.42169
55 5D9G GLU ASN LEU TYR PHE GLN 0.01091 0.41436 5.69106
56 4RYV ZEA 0.01151 0.40891 5.80645
57 1GKZ ADP 0.00001418 0.51581 5.85366
58 4P5Z Q7M 0.01181 0.41233 5.85366
59 3JQ3 ADP 0.0141 0.40463 5.85366
60 4WGF HX2 0.005869 0.43921 6.34146
61 4MJ0 BGC SIA SIA GAL 0.01473 0.41578 6.34146
62 4MJ0 SIA SIA GAL 0.01752 0.41154 6.34146
63 5HCY 60D 0.02646 0.40065 6.34146
64 1YC4 43P 0.000009864 0.54915 7.31707
65 1Q19 SSC 0.007451 0.42846 7.31707
66 3NMQ 7PP 0.000401 0.46811 7.80488
67 3D36 ADP 0.0004193 0.45268 7.80488
68 3DLG GWE 0.03769 0.40551 7.80488
69 4WOE ADP 0.00375 0.44595 8.29268
70 3EHH ADP 0.008116 0.42074 8.29268
71 4KQP GLN 0.01736 0.41059 8.29268
72 5KF6 FAD 0.007996 0.41185 8.78049
73 4MOB ADP 0.01289 0.41846 9.26829
74 4HXY ACA 0.02296 0.41538 9.26829
75 2NZ2 CIR 0.02249 0.40289 9.26829
76 1Y8O ADP 0.00006453 0.51749 11.7073
77 3H4L ANP 0.0001412 0.45788 11.7073
78 2F6U CIT 0.01645 0.40986 12.1951
79 4GCZ ADP 0.002691 0.42185 12.6829
80 5L2J 70E 0.02667 0.41539 12.6829
81 5L2J 6UL 0.02525 0.41539 12.6829
82 2GTF P1R 0.002735 0.44263 12.7778
83 2XCM ADP 0.0001006 0.49567 13.0435
84 3EHG ATP 0.009573 0.40867 13.2812
85 1TH8 ADP 0.0003996 0.47934 13.6585
86 1I58 ADP 0.00006292 0.50503 14.2857
87 1I58 ACP 0.0006631 0.43066 14.2857
88 4O8A FAD 0.01004 0.4099 16.0976
89 1TIW TFB 0.01572 0.40855 16.5854
90 4IVG ANP 0.001116 0.41015 17.0732
91 4IPE ANP 0.001038 0.40741 17.0732
92 4CQE CQE 0.01841 0.40336 18.5366
93 3CV2 COA 0.002009 0.46287 19.0244
94 1ID0 ANP 0.0003777 0.47474 19.0789
95 1TID ATP 0.0002079 0.47064 20.5882
96 3A0T ADP 0.0002958 0.45918 21.7105
97 1B63 ANP 0.0003151 0.4352 35.6098
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