Receptor
PDB id Resolution Class Description Source Keywords
5CPH 1.2 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYR COMPLEXED WITH A FRAGMENT STAPHYLOCOCCUS AUREUS DNA GYRASE GYRB FRAGMENT-BASED SCREENING STRUCTURE-BASED ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: FRAGMENT-BASED DISCOVERY OF DNA GYRASE INHIBITORS T THE ATPASE SUBUNIT OF GYRB. BIOORG.MED.CHEM.LETT. V. 26 1314 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EVO B:302;
A:301;
Valid;
Valid;
none;
none;
submit data
222.242 C14 H10 N2 O c1ccc...
MPD B:301;
Invalid;
none;
submit data
118.174 C6 H14 O2 C[C@@...
SO4 A:302;
B:303;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TTZ 1.63 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF A TOPOISOMERASE ATPASE INHIBITOR STAPHYLOCOCCUS AUREUS PROTEIN-INHIBITOR COMPLEX ATP-BINDING STRUCTURE-BASED DRUGANTIMICROBIAL ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: PYRROLAMIDE DNA GYRASE INHIBITORS: OPTIMIZATION OF ANTIBACTERIAL ACTIVITY AND EFFICACY. BIOORG.MED.CHEM.LETT. V. 21 7416 2011
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
5 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
6 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
7 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
8 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
9 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
10 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
11 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
12 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
13 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
14 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
15 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
5 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
6 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
7 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
8 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
9 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
10 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
11 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
12 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
13 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
14 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
15 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
16 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
17 6Y8N ic50 = 9 nM OGH C21 H21 F N8 O Cc1ncc(cn1....
18 6Y8L - NOV C31 H36 N2 O11 Cc1c(ccc2c....
19 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
20 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
50% Homology Family (67)
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 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
13 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
14 6YD9 ic50 = 110 nM ON2 C16 H15 Cl2 N5 O2 S Cc1c(c(c([....
15 6F94 ic50 = 0.099 uM D0H C23 H25 N5 O2 CCNC(=O)Nc....
16 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
17 6KZX ic50 = 0.2 uM E0L C18 H15 N3 O4 CNc1cccc2c....
18 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
19 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
20 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
21 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
22 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
23 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
24 6KZZ ic50 = 0.0017 uM E0R C18 H15 N3 O4 CNc1cccc2c....
25 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
26 6F86 ic50 = 0.037 uM CWW C17 H16 Br N7 O2 CCNC(=O)Nc....
27 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
28 6F8J ic50 = 0.086 uM CZ5 C17 H17 N7 O2 CCNC(=O)Nc....
29 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
30 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
31 7C7O ic50 = 0.52 nM FKU C21 H22 F N5 O4 CNc1cc(cc2....
32 7C7N ic50 = 0.36 nM FKR C18 H14 F N3 O4 CNc1cc(cc2....
33 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
34 6F96 ic50 = 0.019 uM D0K C21 H22 N6 O3 CCNC(=O)Nc....
35 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
36 6ENH - BHW C55 H59 N5 O20 Cc1ccc([nH....
37 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
38 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
39 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 6ENG - BHW C55 H59 N5 O20 Cc1ccc([nH....
41 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
42 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
43 4PU9 - ADP BEF n/a n/a
44 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
45 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
47 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
48 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
49 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
50 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
51 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
52 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
53 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
54 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
55 6Y8N ic50 = 9 nM OGH C21 H21 F N8 O Cc1ncc(cn1....
56 6Y8L - NOV C31 H36 N2 O11 Cc1c(ccc2c....
57 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
58 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
59 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
60 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
61 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
62 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
63 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
64 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
65 6M1S Ki < 1 nM EZ9 C26 H23 F4 N7 O3 CCNc1cc(cc....
66 6M1J Ki = 2 nM EZ6 C24 H17 F4 N7 O2 CNc1cc(cc2....
67 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EVO; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 EVO 1 1
2 1TD 0.564516 0.725
3 X2M 0.484375 0.861111
Similar Ligands (3D)
Ligand no: 1; Ligand: EVO; Similar ligands found: 386
No: Ligand Similarity coefficient
1 FNA 0.9711
2 B5A 0.9416
3 5P3 0.9413
4 LL1 0.9394
5 TRP 0.9348
6 DXK 0.9331
7 HA6 0.9325
8 8G6 0.9302
9 LQG 0.9290
10 LR2 0.9284
11 6PB 0.9276
12 6J9 0.9275
13 25O 0.9272
14 BZM 0.9270
15 5NN 0.9267
16 F40 0.9266
17 536 0.9265
18 3B4 0.9261
19 9F8 0.9250
20 QZ8 0.9249
21 LI7 0.9239
22 ITW 0.9233
23 ZME 0.9227
24 CUT 0.9221
25 C4E 0.9218
26 5V7 0.9218
27 DTR 0.9209
28 FUZ 0.9207
29 7ZL 0.9206
30 1X8 0.9201
31 3GX 0.9183
32 7VY 0.9182
33 ELH 0.9181
34 12R 0.9178
35 9CE 0.9176
36 CC5 0.9168
37 96R 0.9150
38 5F8 0.9133
39 5FL 0.9132
40 ZEA 0.9132
41 Q5M 0.9130
42 AEY 0.9124
43 848 0.9124
44 P9I 0.9113
45 M02 0.9111
46 54X 0.9110
47 XFE 0.9107
48 96Z 0.9106
49 ZEZ 0.9106
50 HWH 0.9104
51 II4 0.9096
52 0LO 0.9093
53 LI4 0.9092
54 S7V 0.9084
55 M5H 0.9078
56 P4L 0.9077
57 3IP 0.9073
58 MW5 0.9071
59 3IL 0.9063
60 5WN 0.9054
61 MFR 0.9054
62 HHV 0.9051
63 QUB 0.9051
64 5WT 0.9051
65 W8L 0.9047
66 2L2 0.9045
67 1Q4 0.9043
68 NWD 0.9041
69 YEX 0.9027
70 W8G 0.9026
71 IQQ 0.9025
72 6XC 0.9024
73 NIY 0.9022
74 ID8 0.9020
75 C0W 0.9016
76 EXR 0.9016
77 7NU 0.9014
78 CDJ 0.9014
79 H35 0.9014
80 692 0.9013
81 VM1 0.9011
82 7L4 0.9009
83 TLF 0.9007
84 IBC 0.9005
85 5JT 0.9004
86 MBP 0.9003
87 AMR 0.9000
88 2H4 0.8999
89 LTN 0.8997
90 L5D 0.8996
91 NPL 0.8993
92 A73 0.8988
93 H2W 0.8988
94 3D8 0.8986
95 ALN 0.8985
96 5B2 0.8984
97 2L1 0.8983
98 Q4G 0.8982
99 22T 0.8980
100 KYN 0.8976
101 AVA 0.8975
102 MNX 0.8975
103 GWD 0.8974
104 HVE 0.8972
105 2GQ 0.8970
106 2NJ 0.8970
107 RVE 0.8963
108 G6P 0.8960
109 AUV 0.8959
110 TQU 0.8957
111 5E4 0.8956
112 ASE 0.8956
113 VT3 0.8947
114 NKI 0.8947
115 KWB 0.8943
116 LVP 0.8941
117 RGK 0.8939
118 JR2 0.8938
119 8RK 0.8934
120 8HH 0.8931
121 OX2 0.8929
122 M3W 0.8929
123 IOP 0.8928
124 LLG 0.8927
125 5TZ 0.8927
126 YE7 0.8926
127 CUH 0.8926
128 3Y7 0.8925
129 XEZ 0.8923
130 KF5 0.8921
131 WUB 0.8920
132 1V1 0.8920
133 AYS 0.8917
134 67Y 0.8917
135 3EB 0.8917
136 I46 0.8916
137 29B 0.8916
138 20D 0.8915
139 96U 0.8915
140 AKD 0.8914
141 56N 0.8911
142 JHY 0.8909
143 25F 0.8907
144 23N 0.8906
145 AJD 0.8903
146 DFL 0.8900
147 EYA 0.8898
148 CPW 0.8895
149 57D 0.8893
150 HH6 0.8890
151 E9L 0.8889
152 M01 0.8887
153 9BF 0.8886
154 D1G 0.8884
155 FER 0.8882
156 GZV 0.8878
157 BQ5 0.8877
158 78U 0.8876
159 2LX 0.8876
160 NYJ 0.8873
161 GNV 0.8869
162 CX4 0.8868
163 3WJ 0.8867
164 6DQ 0.8866
165 ZYW 0.8864
166 BJ4 0.8863
167 CZ0 0.8863
168 BIO 0.8863
169 GAT 0.8860
170 0DF 0.8860
171 3F4 0.8859
172 4Z9 0.8858
173 2UD 0.8856
174 3IB 0.8855
175 2KU 0.8853
176 0FS 0.8853
177 HKK 0.8852
178 4OG 0.8852
179 5E5 0.8850
180 B4L 0.8850
181 S1D 0.8849
182 JSX 0.8849
183 QMS 0.8843
184 1V4 0.8843
185 7I2 0.8842
186 LWS 0.8841
187 7AP 0.8841
188 8WZ 0.8840
189 VBC 0.8839
190 D87 0.8836
191 CHQ 0.8835
192 KMP 0.8833
193 0FR 0.8831
194 I2E 0.8828
195 NFZ 0.8828
196 EYM 0.8826
197 ZIQ 0.8825
198 B21 0.8822
199 HNA 0.8821
200 NEU 0.8816
201 MXD 0.8815
202 EXL 0.8815
203 FCD 0.8815
204 SZ5 0.8812
205 QR2 0.8811
206 MPU 0.8811
207 PLP 0.8809
208 C9E 0.8809
209 EYY 0.8808
210 SGW 0.8807
211 ZYV 0.8805
212 3CA 0.8805
213 CU5 0.8804
214 2QU 0.8803
215 ETV 0.8802
216 TQ1 0.8801
217 AC2 0.8800
218 36Z 0.8799
219 6J3 0.8798
220 BZQ 0.8797
221 EWG 0.8797
222 CTE 0.8796
223 1QV 0.8794
224 NXB 0.8794
225 ONZ 0.8792
226 8DA 0.8792
227 7R4 0.8789
228 9UL 0.8788
229 DE7 0.8786
230 774 0.8785
231 5E1 0.8785
232 WLH 0.8777
233 F52 0.8777
234 LFQ 0.8776
235 BPY 0.8776
236 B4O 0.8774
237 ZRL 0.8771
238 JYW 0.8771
239 ML1 0.8771
240 TR7 0.8770
241 PIQ 0.8768
242 PTB 0.8767
243 LLT 0.8767
244 ML2 0.8766
245 CFK 0.8766
246 T28 0.8766
247 U19 0.8764
248 1AJ 0.8764
249 S46 0.8764
250 2JK 0.8763
251 49P 0.8758
252 MUR 0.8757
253 55D 0.8755
254 3M8 0.8755
255 0OM 0.8754
256 1VK 0.8752
257 AZY 0.8752
258 2T4 0.8752
259 UKV 0.8750
260 O9Z 0.8746
261 JY2 0.8743
262 MG7 0.8743
263 BG6 0.8741
264 AUY 0.8739
265 1V3 0.8739
266 LEL 0.8737
267 EY7 0.8736
268 1QP 0.8736
269 1Z8 0.8736
270 2AN 0.8736
271 KED 0.8735
272 CMU 0.8732
273 3WL 0.8729
274 0RY 0.8728
275 SNB 0.8726
276 0H5 0.8726
277 2VQ 0.8723
278 3SU 0.8722
279 B2E 0.8722
280 RKV 0.8722
281 C0Y 0.8712
282 JF5 0.8710
283 GXD 0.8709
284 92O 0.8709
285 5DN 0.8708
286 TH4 0.8707
287 MUX 0.8705
288 BHF 0.8704
289 2D2 0.8703
290 C09 0.8701
291 6J5 0.8699
292 A3Q 0.8698
293 B61 0.8697
294 34L 0.8696
295 BXZ 0.8695
296 GXG 0.8694
297 JP2 0.8693
298 CUQ 0.8691
299 1EL 0.8690
300 KLK 0.8690
301 ABJ 0.8690
302 TCR 0.8686
303 43U 0.8681
304 SQM 0.8679
305 JRO 0.8679
306 78P 0.8679
307 QEI 0.8675
308 9AP 0.8672
309 GG5 0.8670
310 KYA 0.8670
311 XYP XIF 0.8667
312 MEX 0.8665
313 DK1 0.8662
314 27M 0.8662
315 SLY 0.8661
316 XIF XYP 0.8661
317 NQ7 0.8661
318 NRA 0.8661
319 WCU 0.8660
320 OSB 0.8659
321 BN1 0.8658
322 O9Q 0.8657
323 363 0.8654
324 78Y 0.8650
325 64E 0.8649
326 TCC 0.8649
327 FT6 0.8648
328 PXP 0.8647
329 91F 0.8647
330 3C3 0.8645
331 2P3 0.8644
332 NU3 0.8642
333 9RM 0.8640
334 JCZ 0.8638
335 TXQ 0.8638
336 T6Z 0.8634
337 2GD 0.8634
338 L07 0.8630
339 K80 0.8629
340 TIA 0.8629
341 9OF 0.8629
342 GA2 0.8628
343 YE6 0.8627
344 A5H 0.8626
345 U7E 0.8625
346 O9T 0.8625
347 GHQ 0.8624
348 ANC 0.8623
349 BGU 0.8622
350 IQZ 0.8622
351 BY5 0.8621
352 EQA 0.8620
353 IDZ 0.8620
354 IQ5 0.8619
355 3L1 0.8616
356 KLV 0.8614
357 3WK 0.8614
358 XZ8 0.8612
359 4R1 0.8612
360 M9N 0.8609
361 Q0K 0.8607
362 BZS 0.8606
363 AGI 0.8606
364 B2T 0.8603
365 UI2 0.8601
366 28S 0.8595
367 SYR 0.8593
368 CKA 0.8590
369 5I5 0.8590
370 3WO 0.8587
371 3WN 0.8587
372 11G 0.8586
373 SXX 0.8585
374 64C 0.8580
375 XG1 0.8576
376 4KL 0.8572
377 5WS 0.8571
378 272 0.8560
379 JXT 0.8553
380 7MX 0.8549
381 DNC 0.8545
382 790 0.8541
383 DBQ 0.8539
384 GRX 0.8539
385 FYJ 0.8531
386 64F 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TTZ; Ligand: 07N; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3ttz.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3TTZ; Ligand: 07N; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3ttz.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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