Receptor
PDB id Resolution Class Description Source Keywords
4CC6 2.01 Å EC: 6.5.1.2 FRAGMENT-BASED DISCOVERY OF 6 AZAINDAZOLES AS INHIBITORS OF BACTERIAL DNA LIGASE STAPHYLOCOCCUS AUREUS LIGASE LIGA ANTIBIOTIC DESIGN
Ref.: FRAGMENT-BASED DISCOVERY OF 6-AZAINDAZOLES AS INHIB BACTERIAL DNA LIGASE. ACS MED.CHEM.LETT. V. 4 1208 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1310;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
L5Y A:1311;
Valid;
none;
ic50 = 0.23 uM
323.273 C14 H12 F3 N5 O c1cnc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CC6 2.01 Å EC: 6.5.1.2 FRAGMENT-BASED DISCOVERY OF 6 AZAINDAZOLES AS INHIBITORS OF BACTERIAL DNA LIGASE STAPHYLOCOCCUS AUREUS LIGASE LIGA ANTIBIOTIC DESIGN
Ref.: FRAGMENT-BASED DISCOVERY OF 6-AZAINDAZOLES AS INHIB BACTERIAL DNA LIGASE. ACS MED.CHEM.LETT. V. 4 1208 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FPO - 10L C7 H7 N3 c1cc2cn[nH....
2 5FPR - LGA C4 H5 N3 c1cnc(nc1)....
3 4CC6 ic50 = 0.23 uM L5Y C14 H12 F3 N5 O c1cncc2c1c....
4 4CC5 Kd = 38 uM L5V C6 H4 Cl N5 c1c(nc(cn1....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1TA8 - NMN C11 H16 N2 O8 P c1cc(c[n+]....
2 4LH7 ic50 = 34 uM 1X8 C9 H8 N4 O2 S c1c2c(c(cn....
3 4LH6 ic50 = 77 uM 1X7 C8 H6 Br N3 O S c1c2c(c(cn....
4 5FPO - 10L C7 H7 N3 c1cc2cn[nH....
5 5FPR - LGA C4 H5 N3 c1cnc(nc1)....
6 4CC6 ic50 = 0.23 uM L5Y C14 H12 F3 N5 O c1cncc2c1c....
7 4CC5 Kd = 38 uM L5V C6 H4 Cl N5 c1c(nc(cn1....
8 4GLW Kd = 0.8 uM 0XT C8 H10 N6 O Cc1c(nc2c(....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1TA8 - NMN C11 H16 N2 O8 P c1cc(c[n+]....
2 4LH7 ic50 = 34 uM 1X8 C9 H8 N4 O2 S c1c2c(c(cn....
3 4LH6 ic50 = 77 uM 1X7 C8 H6 Br N3 O S c1c2c(c(cn....
4 5FPO - 10L C7 H7 N3 c1cc2cn[nH....
5 5FPR - LGA C4 H5 N3 c1cnc(nc1)....
6 4CC6 ic50 = 0.23 uM L5Y C14 H12 F3 N5 O c1cncc2c1c....
7 4CC5 Kd = 38 uM L5V C6 H4 Cl N5 c1c(nc(cn1....
8 4GLW Kd = 0.8 uM 0XT C8 H10 N6 O Cc1c(nc2c(....
9 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
10 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
11 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: L5Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 L5Y 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4CC6; Ligand: L5Y; Similar sites found: 235
This union binding pocket(no: 1) in the query (biounit: 4cc6.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DLS ADP 0.00004518 0.52411 0.943396
2 4UWH JXM 0.002007 0.44413 1.25786
3 4AUA 4AU 0.001378 0.45444 1.30293
4 5UIU 8CG 0.002055 0.46568 1.57233
5 4I6H 1C8 0.004759 0.43023 1.62338
6 4L3L 5FI 0.01352 0.42344 1.64474
7 1VJY 460 0.006592 0.44217 1.65016
8 4YZN 4K5 0.01635 0.41068 1.74216
9 4JDI ANP 0.01005 0.41795 1.88679
10 3HMO STU 0.008332 0.4162 1.88679
11 5VSM 5AD 0.02277 0.40016 1.88679
12 5N87 N66 0.03899 0.40498 1.91693
13 1IOW PHY 0.0006092 0.49866 1.96078
14 1IOW ADP 0.0006092 0.49866 1.96078
15 3HAV ATP 0.0000249 0.50116 2.00669
16 4D2S DYK 0.007501 0.414 2.11268
17 5M06 ADP 0.01079 0.40859 2.17391
18 4IX4 ADP 0.0001742 0.50557 2.20126
19 5W4W 9WG 0.003303 0.45643 2.20126
20 2GU8 796 0.009631 0.45268 2.20126
21 5VZ0 ADP 0.001582 0.45151 2.20126
22 4XH0 ADP 0.001421 0.45056 2.20126
23 4CLI 5P8 0.01091 0.44137 2.20126
24 4WB6 ATP 0.006365 0.43611 2.20126
25 1RE8 BD2 0.01511 0.43554 2.20126
26 4Y0X ADP 0.003333 0.43342 2.20126
27 5MY8 RXZ 0.01021 0.42415 2.20126
28 3ALN ANP 0.009142 0.42001 2.20126
29 3PTG 932 0.004821 0.41815 2.20126
30 4KBA 1QM 0.004909 0.41777 2.20126
31 5JFS 6K0 0.0005591 0.50698 2.27273
32 5MJA 7O3 0.005245 0.42815 2.29508
33 5CEO 50D 0.008556 0.41767 2.33333
34 4LRJ ANP 0.008568 0.41561 2.36686
35 2QCS ANP 0.01011 0.42586 2.4055
36 4FL3 ANP 0.001853 0.45646 2.51572
37 3OFM 4B0 0.001501 0.44775 2.51572
38 2PVN P63 0.004586 0.44631 2.51572
39 1CM8 ANP 0.00227 0.44385 2.51572
40 3HZT J60 0.002599 0.42374 2.51572
41 3TXO 07U 0.006613 0.41895 2.51572
42 3AQV TAK 0.001445 0.45569 2.53623
43 4FG8 ATP 0.02036 0.4026 2.53968
44 5UR1 YY9 0.007811 0.4482 2.57235
45 4YMJ 4EJ 0.0005199 0.47326 2.63158
46 3FW3 GLC 0.007421 0.43097 2.63158
47 5IH1 GDP 0.009726 0.4493 2.64901
48 5IH1 6BQ 0.009726 0.4493 2.64901
49 3RE4 TO1 0.009534 0.40657 2.71318
50 4AGQ P96 0.02565 0.40077 2.73973
51 1CKN GTP 0.0000231 0.52833 2.83019
52 3KAL ADP 0.0006318 0.49646 2.83019
53 3V4S ADP 0.0007276 0.49596 2.83019
54 3V4S ATP 0.0003692 0.49146 2.83019
55 2QK4 ATP 0.0002274 0.48117 2.83019
56 1CKM GTP 0.000007616 0.46666 2.83019
57 3PE2 E1B 0.006628 0.45486 2.83019
58 5AWM ANP 0.0005049 0.45465 2.83019
59 4USF 6UI 0.003325 0.44726 2.83019
60 4YZC STU 0.01492 0.42818 2.83019
61 2Z7R STU 0.01603 0.4095 2.83019
62 5HVJ ANP 0.005498 0.42261 2.85714
63 3SRV S19 0.002722 0.43999 2.88809
64 5HES 032 0.0006508 0.47917 2.9316
65 4AU8 Z3R 0.00307 0.43019 3.04054
66 3O0G 3O0 0.002476 0.442 3.08219
67 1UNH IXM 0.002856 0.43427 3.08219
68 2Y6O 1N1 0.003513 0.44256 3.09278
69 2CFM AMP 0.00001009 0.53149 3.14465
70 5AX9 4KT 0.001869 0.45021 3.14465
71 1Q8Y ADE 0.001795 0.43856 3.14465
72 2V7O DRN 0.002406 0.4325 3.14465
73 4K38 SAM 0.009211 0.41801 3.14465
74 4K39 SAM 0.009964 0.4144 3.14465
75 5I35 ANP 0.001332 0.41327 3.14465
76 4K37 SAM 0.01248 0.40759 3.14465
77 4AZT LY2 0.005202 0.41027 3.16344
78 5K2M ADP 0.002516 0.45337 3.2967
79 3GGF GVD 0.008478 0.41369 3.32226
80 2VN9 GVD 0.007268 0.40966 3.32226
81 5DEY 59T 0.02428 0.42911 3.367
82 3ORQ ADP 0.0001712 0.50594 3.45912
83 3VOT ADP 0.0001917 0.48786 3.45912
84 4U44 3D9 0.002097 0.44774 3.45912
85 1M0W ANP 0.004914 0.42522 3.45912
86 2WQN ADP 0.001787 0.42207 3.54839
87 5BVE 4VG 0.02414 0.43409 3.60111
88 5IQD RIO 0.006273 0.44915 3.60656
89 5IQD GNP 0.005977 0.44915 3.60656
90 4O4F IHP 0.009951 0.4262 3.62903
91 4O4F ATP 0.009307 0.4262 3.62903
92 4PZ6 GMP 0.000004208 0.51811 3.77358
93 2VPQ ANP 0.001471 0.46334 3.77358
94 3AKK ADP 0.001186 0.4621 3.77358
95 5DXT 5H5 0.001586 0.45586 3.77358
96 3LXK MI1 0.003155 0.45318 3.77358
97 4NM5 ADP 0.002476 0.45198 3.77358
98 5FI4 5XV 0.00285 0.45064 3.77358
99 3F7Z 34O 0.001935 0.44946 3.77358
100 2JLD AG1 0.005331 0.44822 3.77358
101 5MW8 ATP 0.003897 0.44208 3.77358
102 3GC0 AMP 0.001927 0.42174 3.77358
103 2PYW ADP 0.009943 0.41818 3.77358
104 3WVR AMP 0.001885 0.41461 3.77358
105 4BCN T9N 0.0005392 0.44381 3.81679
106 4CFU 2WC 0.0004724 0.43788 3.81679
107 4BCQ TJF 0.00482 0.4208 3.81679
108 1H2T GDP 7MG 0.0142 0.40483 3.84615
109 4H3Q ANP 0.003635 0.4436 3.8674
110 4H3P ANP 0.00215 0.40114 3.8674
111 4A4X JUP 0.001235 0.47238 3.94265
112 1ZY5 ANP 0.001415 0.45388 3.9604
113 3KRR DQX 0.00975 0.45734 4.0678
114 3E7O 35F 0.004478 0.44959 4.08805
115 4JR7 GNP 0.00194 0.44941 4.08805
116 5U6C 7YS 0.002818 0.44736 4.08805
117 5IVE 6E8 0.01893 0.41708 4.08805
118 5CKW ANP 0.008208 0.4097 4.08805
119 5TT6 ATP 0.000295 0.40555 4.08805
120 3SXS PP2 0.004297 0.43635 4.10448
121 1W2D ADP 0.005476 0.40721 4.15094
122 4X7Q 3YR 0.002305 0.41218 4.16667
123 3NW7 LGV 0.01179 0.44138 4.23453
124 1XDN ATP 0.000003747 0.57659 4.33213
125 4I94 ANP 0.002589 0.44106 4.33333
126 1K3A ACP 0.005427 0.4208 4.34783
127 3DNT ATP 0.0002591 0.50318 4.40252
128 1T36 ADP 0.007256 0.43466 4.40252
129 4CYI ATP 0.008456 0.42169 4.40252
130 5DBX ANP 0.006941 0.41563 4.40252
131 3TPV ADE 0.0006 0.40786 4.40252
132 4O1P ANP 0.01688 0.40113 4.40252
133 3FHI ANP 0.01408 0.41848 4.54545
134 1BYG STU 0.003791 0.40062 4.67626
135 4YLL 4E3 0.01973 0.40655 4.70914
136 4QTB 38Z 0.002926 0.45634 4.71698
137 5EOB 5QQ 0.0131 0.44459 4.71698
138 4LOO SB4 0.00685 0.42243 4.71698
139 4TWP AXI 0.009957 0.44443 4.79705
140 3KMW ATP 0.006611 0.42113 4.79705
141 4M69 ANP 0.005255 0.432 4.947
142 4OCJ NDG 0.001014 0.4909 5.03145
143 4N70 2HX 0.001891 0.48608 5.03145
144 5LPZ ADP 0.001338 0.45734 5.03145
145 5TO8 7FM 0.005092 0.45503 5.03145
146 4OH4 ANP 0.002189 0.44683 5.03145
147 3V8S 0HD 0.002612 0.40407 5.03145
148 4BKJ STI 0.001314 0.46934 5.07937
149 3BRN SRO 0.01522 0.40073 5.09554
150 3DAK ANP 0.006893 0.4223 5.17241
151 5VC5 96M 0.002788 0.45593 5.19031
152 4Q5H ANP 0.005453 0.42732 5.26316
153 4U98 ACP 0.001103 0.41212 5.28634
154 2Q7D ANP 0.0001152 0.5248 5.34591
155 1I7L ATP 0.0002611 0.50301 5.34591
156 5C03 AGS 0.0004785 0.4793 5.34591
157 2JDR L20 0.01631 0.44082 5.34591
158 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.01631 0.44082 5.34591
159 4OUC 5ID 0.007175 0.41722 5.34591
160 2YW2 ATP 0.0005246 0.40938 5.34591
161 2PZI AXX 0.004108 0.40691 5.34591
162 4WOV 3SM 0.001706 0.42378 5.36278
163 5LPB ADP 0.001584 0.44397 5.40541
164 2YNE NHW 0.04229 0.43113 5.66038
165 2YNE YNE 0.04229 0.43113 5.66038
166 3K5I ADP 0.01075 0.4165 5.66038
167 3K5I AIR 0.02047 0.4165 5.66038
168 4IZY 1J2 0.0005184 0.4064 5.66038
169 2B9H ADP 0.007347 0.42288 5.66572
170 2B9F ADP 0.007122 0.4216 5.66572
171 2B9J ADP 0.01642 0.40172 5.66572
172 2ZV2 609 0.001259 0.43654 5.7047
173 5A89 FMN 0.01833 0.42925 5.76923
174 5A89 ADP 0.01833 0.42925 5.76923
175 3TY5 ADP 0.00003182 0.53151 5.97484
176 3TY5 ATP 0.0006001 0.46414 5.97484
177 3X01 AMP 0.00369 0.43245 5.97484
178 1OX5 1PR 0.01282 0.42333 5.97484
179 4OCV ANP 0.0002633 0.42268 5.97484
180 4MV1 ADP 0.03032 0.40754 5.97484
181 3JVH HHV 0.01166 0.43047 6.01093
182 4NST ADP 0.002414 0.44474 6.28931
183 5A3T MMK 0.03061 0.40617 6.28931
184 2GQR ADP 0.009743 0.41287 6.32911
185 4XV1 904 0.005346 0.44815 6.60377
186 5EFQ ADP 0.002704 0.44232 6.60377
187 2V58 LZJ 0.0184 0.43004 6.60377
188 4CQE CQE 0.008694 0.42285 6.60377
189 4WW7 AMP 0.00371 0.44138 6.89655
190 5TDF ADP 0.0007782 0.47326 6.91824
191 5LI1 ANP 0.008963 0.42219 6.91824
192 4DC2 ADE 0.001299 0.41971 6.91824
193 5H2U 1N1 0.003062 0.40315 7.11611
194 5DA3 58V 0.006921 0.40374 7.16981
195 3MVH WFE 0.006901 0.43854 7.2327
196 1EHI ADP 0.0002467 0.41902 7.2327
197 1JPA ANP 0.001227 0.41997 7.37179
198 2A19 ANP 0.003102 0.41929 7.42857
199 4P5Z Q7M 0.02399 0.41825 7.54717
200 5USZ SKE 0.0006597 0.48792 7.61246
201 3UDZ ADP 0.002285 0.44801 7.70791
202 4Y8D 49J 0.002447 0.43764 7.85714
203 5COU ATP 0.000005794 0.57054 7.86164
204 4G17 0VN 0.0005449 0.47163 7.86164
205 4IDT T28 0.01129 0.40972 7.86164
206 4AZW ATP 0.0005756 0.47977 8.1761
207 2PUL ACP 0.01173 0.40891 8.1761
208 5FBN 5WF 0.006762 0.44403 8.48709
209 4DFU QUE 0.0008474 0.46014 9.1195
210 4R78 AMP 0.002694 0.43017 9.38511
211 3ETH ATP 0.0006575 0.47894 9.43396
212 5HQ0 LZ9 0.002192 0.4509 9.52381
213 1S68 AMP 0.000003242 0.55615 9.63855
214 5LMK 6ZK 0.009214 0.41193 9.74843
215 4CRL C1I 0.003179 0.45993 9.82456
216 5W2I ADP 0.0193 0.40856 10.1167
217 5W2I I3P 0.0193 0.40856 10.1167
218 5DZT AMP 0.0001146 0.47687 10.6918
219 3VPB ADP 0.0007008 0.48318 10.7143
220 4XYM A12 0.001254 0.46089 10.8696
221 5C1P DAL DAL 0.0004347 0.49369 11.1111
222 5C1P ADP 0.0002437 0.48582 11.1111
223 5C4L 4XR 0.0005376 0.4972 11.215
224 5C4L SIS 0.00306 0.45815 11.215
225 2WU6 DKI 0.006037 0.43252 11.3208
226 3TII ANP 0.008388 0.40925 11.3208
227 4BCM T7Z 0.0003738 0.46417 11.8321
228 3GNI ATP 0.006719 0.42668 12.5786
229 3RI1 3RH 0.005897 0.4378 12.7796
230 4BTK DTQ 0.003746 0.43535 12.8931
231 4NFN 2KC 0.002211 0.44441 13.2686
232 4F9C 0SX 0.002776 0.43958 15.9722
233 4ZGP ADP 0.009595 0.41319 16.7235
234 2BKK ADP 0.004368 0.42535 21.9697
235 3ZRM ZRM 0.0008881 0.4661 28.125
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