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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 (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
2 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
3 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
4 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
5 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
6 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
7 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
8 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
9 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
10 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
11 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
12 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
13 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
2 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
3 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
4 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
5 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
6 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
7 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
8 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
9 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
10 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
11 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
12 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
13 5Z9F - AX7 C7 H7 N3 c1ccc2c(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: CBN; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 CBN 1 1
2 NOV 0.669291 0.820895
3 CZJ 0.422535 0.73913
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KZN; Ligand: CBN; Similar sites found with APoc: 263
This union binding pocket(no: 1) in the query (biounit: 1kzn.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5UGW GSH None
2 1M48 FRG None
3 5CLO NS8 None
4 5NNT DPV None
5 1NU4 MLA None
6 2D6M LBT None
7 1P0Z FLC None
8 4WG0 CHD None
9 3RET PYR None
10 1NF8 BOG 0.97561
11 6C5F 7L9 1.7094
12 2GFD RDA 1.95122
13 6D28 NEC 1.95122
14 3EFS BTN 1.95122
15 2QHV OC9 1.95122
16 1BGQ RDC 2.43902
17 3C3D FO1 2.43902
18 3BMN AX3 2.43902
19 1XMY ROL 2.43902
20 3JU6 ANP 2.43902
21 1H5R G1P 2.43902
22 3G58 988 2.43902
23 1VRP ADP 2.43902
24 2QHS OCA 2.43902
25 3CBC DBS 2.52525
26 6F3G CJN 2.71186
27 5FIT AP2 2.72109
28 1QKQ MAN 2.8169
29 2O1V ADP 2.92683
30 3WXL ADP 2.92683
31 5KJW 53C 2.92683
32 1F9V ADP 2.92683
33 5YJS SAL 2.92683
34 4WHZ 3NL 2.92683
35 3QSB 743 2.92683
36 1J2Z SOG 2.92683
37 4Y9T PA1 2.92683
38 3O01 DXC 2.92683
39 1M2Z BOG 2.92683
40 5MJA 7O3 2.92683
41 3G5N PB2 2.92683
42 1B5E DCM 2.92683
43 6GNO XDI 2.96296
44 1YP1 LYS ASN LEU 2.9703
45 4K7O EKZ 2.97619
46 4IEN GDP 3.06748
47 1P6O HPY 3.10559
48 3SAO DBH 3.125
49 3SAO NKN 3.125
50 3QXV MTX 3.1746
51 4B7P 9UN 3.41463
52 2YI0 YI0 3.41463
53 3K60 ADP 3.41463
54 2PNC CLU 3.41463
55 5M37 9SZ 3.41463
56 5H2U 1N1 3.41463
57 1Y7P RIP 3.41463
58 5XJD 87L 3.41463
59 5BVE 4VG 3.41463
60 2QBU SAH 3.41463
61 3QPB URA 3.41463
62 5MOB A8S 3.41463
63 6AP6 TLF 3.41463
64 4AVB CMP 3.41463
65 5L1O 7PF 3.41463
66 4CSD MFU 3.41463
67 4J25 OGA 3.41463
68 4KRG OPE 3.41463
69 2VQ5 HBA 3.48259
70 5OCG 9R5 3.7037
71 1RL4 BRR 3.7234
72 4MNS 2AX 3.77358
73 1GT4 UNA 3.77358
74 2PFC PLM 3.82514
75 5UC4 83S 3.90244
76 2VDF OCT 3.90244
77 3TDC 0EU 3.90244
78 4BIX ADP 3.90244
79 5EW9 5VC 3.90244
80 2PYY GLU 3.90244
81 4URF 1PS 3.90244
82 1C5C TK4 3.90244
83 1NCE UMP 3.90244
84 1UNB AKG 3.90244
85 6BR8 PGV 3.90244
86 1V8B ADN 3.90244
87 1AIQ UMP 3.90244
88 6BR9 6OU 3.90244
89 4UDK BMA 3.90244
90 1TLC DGP 3.90244
91 1E4I NFG 3.90244
92 1DDU DDU 3.90244
93 2AAZ UMP 3.90244
94 5OF9 ANP 3.90244
95 5NM7 GLY 3.90244
96 1ZPR UMP 3.90244
97 4K55 H6P 4.03226
98 6FA4 D1W 4.04624
99 4RF7 ARG 4.39024
100 5F5R ANP 4.39024
101 2C2A ADP 4.39024
102 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.39024
103 4XCL AGS 4.39024
104 5Y3N 8MF 4.39024
105 4FFG 0U8 4.39024
106 5TV6 PML 4.39024
107 6F5W KG1 4.39024
108 1ZPD CIT 4.39024
109 1SLT NDG GAL 4.47761
110 2GBB CIT 4.48718
111 1RM8 BAT 4.73373
112 4KBA 1QM 4.87805
113 3NZ1 3NY 4.87805
114 1BRW URA 4.87805
115 3G08 FEE 4.87805
116 6EK3 OUL 4.87805
117 2AG4 OLA 4.87805
118 2AG4 LP3 4.87805
119 5DEX GLY 4.87805
120 1JT2 FER 4.87805
121 3ZF8 GDP 4.87805
122 3VKX T3 4.87805
123 3QDY CBS 4.8951
124 1RYD GLC 4.90956
125 3KO0 TFP 4.9505
126 5IDM ANP 5.02793
127 6FS0 E4W 5.03145
128 1MFI FHC 5.26316
129 5FUI APY 5.30303
130 3AQT RCO 5.36585
131 3DOO SKM 5.36585
132 2IOR ADP 5.36585
133 5W5R PYR 5.36585
134 3V1S 0LH 5.36585
135 4RKS MEV 5.36585
136 4DO1 ANN 5.36585
137 1SDW IYT 5.36585
138 5HWV MBN 5.38462
139 4IN9 SER TRP PHE PRO 5.42169
140 5L8N 6RQ 5.46875
141 3G4Q MCH 5.47945
142 6F7X MFU 5.55556
143 1PWB GLC 5.64972
144 5K21 6QF 5.67376
145 5D9G GLU ASN LEU TYR PHE GLN 5.69106
146 3E85 BSU 5.6962
147 1Y9Q MED 5.72917
148 4RYV ZEA 5.80645
149 5VM6 9EG 5.83942
150 1GKZ ADP 5.85366
151 3JQ3 ADP 5.85366
152 1K0E TRP 5.85366
153 4GID 0GH 5.85366
154 5IM3 DTP 5.85366
155 3IWD M2T 5.88235
156 1A78 TDG 5.97015
157 4WGF HX2 6.34146
158 4MJ0 SIA SIA GAL 6.34146
159 5OSW DIU 6.34146
160 2DXU BT5 6.34146
161 5CWA 0GA 6.34146
162 1KJ1 MAN 6.42202
163 5H9Q TD2 6.45161
164 6CED EYA 6.54206
165 1ZNY GDP 6.82927
166 5LUN OGA 6.82927
167 5OF1 SAL 6.82927
168 5FPE 3TR 6.82927
169 5DQ8 FLF 6.82927
170 5Y4R C2E 6.82927
171 3RF4 FUN 6.89655
172 1EX7 5GP 6.98925
173 2WR9 MAN MAN 7.03125
174 1YC4 43P 7.31707
175 2HK9 SKM 7.31707
176 1W2D ADP 7.31707
177 4OYA 1VE 7.31707
178 3KYF 5GP 5GP 7.31707
179 1I1E DM2 7.31707
180 5XK9 DMA 7.31707
181 5LXT GTP 7.31707
182 5LDQ NAP 7.34463
183 3L5R 47X 7.37705
184 1OYF MHN 7.43802
185 2YMZ LAT 7.69231
186 3D36 ADP 7.80488
187 2Z5Y HRM 7.80488
188 3DLG GWE 7.80488
189 3T1A 5MA 7.80488
190 1T9D PYD 7.80488
191 2PUL ACP 7.80488
192 1KGI T4A 7.87402
193 5DG2 GAL GLC 8.14815
194 1LSH PLD 8.29268
195 3FAL REA 8.29268
196 3EHH ADP 8.29268
197 4WOE ADP 8.29268
198 4KQP GLN 8.29268
199 4OPC FDA 8.29268
200 4OPC PGT 8.29268
201 4M26 AKG 8.29268
202 2GN2 C5P 8.78049
203 1C1D PHE 8.78049
204 1W3T 3GR 8.78049
205 1BXG HCI 8.78049
206 4MOB ADP 9.26829
207 4DE2 DN3 9.26829
208 2NZ2 CIR 9.26829
209 3HYW DCQ 9.26829
210 4HXY ACA 9.26829
211 3E8T UQ8 9.26829
212 4DE3 DN8 9.26829
213 3U7Q HCA 9.26829
214 3X01 AMP 9.26829
215 3R9C ECL 9.26829
216 4YMU ARG 9.7561
217 4GNC ASO 10.2439
218 5DYO FLU 10.2439
219 4NOS ITU 10.2439
220 5WSY 7UC 10.4046
221 4LHD GLY 10.7317
222 6E1Q CFA 10.7317
223 3H4L ANP 11.7073
224 1Y8O ADP 11.7073
225 2P7Q GG6 12.0301
226 5J6A P46 12.1951
227 2F6U CIT 12.1951
228 5OLK DTP 12.1951
229 5G48 1FL 12.6829
230 4GCZ ADP 12.6829
231 5WL1 CUY 12.6829
232 5WL1 D3D 12.6829
233 2Z3U CRR 12.6829
234 5UNJ RJW 12.6829
235 2GTF P1R 12.7778
236 2XCM ADP 13.0435
237 5LX6 78P 13.089
238 3EHG ATP 13.2812
239 1TH8 ADP 13.6585
240 1DTL BEP 13.6646
241 5L2R MLA 14.1463
242 2ZKJ ADP 14.1463
243 1I58 ADP 14.2857
244 1I58 ACP 14.2857
245 1LTT GAL BGC 14.5631
246 5Z84 CHD 15.2941
247 5ZCO CHD 15.2941
248 2AGC DAO 15.4321
249 2Q8G AZX 16.0976
250 1Y75 NAG 16.9492
251 4IVG ANP 17.0732
252 4IPE ANP 17.0732
253 1J3I UMP 17.561
254 1NBU PH2 17.6471
255 3CV2 COA 19.0244
256 1ID0 ANP 19.0789
257 4V1F BQ1 19.7674
258 2Y69 CHD 20
259 1TID ATP 20.5882
260 5LX9 OLB 24.2958
261 5HZ9 5M8 24.4444
262 5N8V KZZ 24.6377
263 1B63 ANP 35.6098
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