Receptor
PDB id Resolution Class Description Source Keywords
6C9Q 1.95 Å EC: 2.7.1.20 MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE BOUND TO 5'-AMIN MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE ANALOG COMPLEX INHIBITOR STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE TB STRUCTURAL GENOMICS CONSORTBSGC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DRUG DESIGN OF 6-SUBSTITUTED ADENO ANALOGUES AS POTENT INHIBITORS OF MYCOBACTERIUM TUB ADENOSINE KINASE. J.MED.CHEM. V. 62 4483 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5N5 A:401;
Valid;
none;
submit data
266.257 C10 H14 N6 O3 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C9V 1.7 Å EC: 2.7.1.20 MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE BOUND TO (2R,3S, (HYDROXYMETHYL)-5-(6-(4-PHENYLPIPERAZIN-1-YL)-9H-PURIN-9-YLT ETRAHYDROFURAN-3,4-DIOL MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE ANALOG COMPLEX INHIBITOR STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE TB STRUCTURAL GENOMICS CONSORTBSGC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DRUG DESIGN OF 6-SUBSTITUTED ADENO ANALOGUES AS POTENT INHIBITORS OF MYCOBACTERIUM TUB ADENOSINE KINASE. J.MED.CHEM. V. 62 4483 2019
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
13 3B1P - NOS C10 H12 N4 O5 c1nc2c(n1[....
14 3B1Q - NOS C10 H12 N4 O5 c1nc2c(n1[....
15 3B1R - AMP MG n/a n/a
16 3B1N - MZR C9 H13 N3 O6 c1nc(c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5N5; Similar ligands found: 302
No: Ligand ECFP6 Tc MDL keys Tc
1 5N5 1 1
2 ADN 0.811321 0.967742
3 RAB 0.811321 0.967742
4 XYA 0.811321 0.967742
5 5CD 0.767857 0.920635
6 A4D 0.767857 0.967742
7 EP4 0.728814 0.880597
8 DTA 0.716667 0.865672
9 M2T 0.716667 0.828571
10 MTA 0.704918 0.878788
11 3DH 0.68254 0.878788
12 DSH 0.666667 0.869565
13 ZAS 0.661538 0.867647
14 A 0.661538 0.816901
15 AMP 0.661538 0.816901
16 LMS 0.661538 0.716049
17 6RE 0.651515 0.857143
18 SRA 0.651515 0.773333
19 5AD 0.649123 0.854839
20 S4M 0.647059 0.789474
21 AOC 0.641791 0.878788
22 J7C 0.632353 0.869565
23 A3N 0.632353 0.953125
24 45A 0.632353 0.794521
25 A2D 0.632353 0.819444
26 ABM 0.632353 0.794521
27 GJV 0.623188 0.84507
28 A12 0.614286 0.786667
29 BA3 0.614286 0.819444
30 MAO 0.614286 0.75641
31 AP2 0.614286 0.786667
32 M33 0.611111 0.808219
33 7D7 0.610169 0.846154
34 Y3J 0.606557 0.828125
35 B4P 0.605634 0.819444
36 AP5 0.605634 0.819444
37 5AS 0.605634 0.714286
38 ADP 0.605634 0.819444
39 SON 0.597222 0.763158
40 A7D 0.597222 0.880597
41 AT4 0.597222 0.786667
42 AN2 0.597222 0.808219
43 ADP MG 0.597222 0.816901
44 MHZ 0.589041 0.779221
45 AU1 0.589041 0.797297
46 ADX 0.589041 0.7375
47 CA0 0.589041 0.797297
48 ATP MG 0.586667 0.816901
49 ADP PO3 0.586667 0.816901
50 A5D 0.586667 0.865672
51 50T 0.581081 0.808219
52 SFG 0.581081 0.850746
53 ATP 0.581081 0.819444
54 5X8 0.581081 0.865672
55 H1Q 0.581081 0.805556
56 HEJ 0.581081 0.819444
57 ACP 0.581081 0.797297
58 KG4 0.581081 0.797297
59 G5A 0.578947 0.714286
60 3AM 0.573529 0.802817
61 APR 0.573333 0.819444
62 5FA 0.573333 0.819444
63 PRX 0.573333 0.773333
64 APC 0.573333 0.786667
65 AQP 0.573333 0.819444
66 AR6 0.573333 0.819444
67 A3G 0.571429 0.938462
68 SA8 0.565789 0.819444
69 RBY 0.565789 0.786667
70 ADV 0.565789 0.786667
71 APC MG 0.565789 0.794521
72 AGS 0.565789 0.776316
73 SAP 0.565789 0.776316
74 AD9 0.565789 0.797297
75 AAT 0.564103 0.84507
76 SAI 0.558442 0.828571
77 SAH 0.558442 0.84058
78 A5A 0.556962 0.698795
79 ANP 0.551282 0.797297
80 ACQ 0.551282 0.797297
81 GAP 0.551282 0.821918
82 T99 0.551282 0.786667
83 TAT 0.551282 0.786667
84 SAM 0.551282 0.773333
85 NEC 0.549296 0.90625
86 3AD 0.546875 0.920635
87 8LE 0.544304 0.753247
88 5AL 0.544304 0.783784
89 EEM 0.544304 0.773333
90 HQG 0.54321 0.808219
91 ATF 0.5375 0.786667
92 ALF ADP 0.5375 0.753247
93 ADP ALF 0.5375 0.753247
94 8X1 0.536585 0.689655
95 53H 0.536585 0.674419
96 2AM 0.536232 0.816901
97 N5A 0.534247 0.892308
98 CC5 0.532258 0.904762
99 VO4 ADP 0.530864 0.783784
100 8LH 0.530864 0.786667
101 6YZ 0.530864 0.797297
102 SSA 0.530864 0.714286
103 ADP VO4 0.530864 0.783784
104 S7M 0.530864 0.773333
105 SRP 0.530864 0.786667
106 SMM 0.530864 0.74359
107 N5O 0.527778 0.893939
108 A3P 0.527027 0.791667
109 52H 0.52439 0.674419
110 VMS 0.52439 0.682353
111 54H 0.52439 0.682353
112 7D5 0.521739 0.756757
113 QQY 0.521127 0.743243
114 5CA 0.518072 0.714286
115 MAP 0.518072 0.776316
116 8LQ 0.518072 0.763158
117 DAL AMP 0.518072 0.783784
118 TSB 0.518072 0.710843
119 A22 0.518072 0.808219
120 OVE 0.513889 0.783784
121 A3S 0.513158 0.923077
122 S8M 0.511905 0.805556
123 9ZA 0.511905 0.74359
124 OZV 0.511905 0.819444
125 8QN 0.511905 0.783784
126 25A 0.511905 0.794521
127 OOB 0.511905 0.783784
128 GEK 0.511905 0.805556
129 9ZD 0.511905 0.74359
130 5SV 0.511905 0.734177
131 A6D 0.511628 0.763158
132 QQX 0.507042 0.733333
133 A1R 0.505882 0.813333
134 LSS 0.505882 0.659091
135 DSZ 0.505882 0.694118
136 ADQ 0.505882 0.821918
137 AMO 0.505882 0.786667
138 4AD 0.505882 0.776316
139 A3R 0.505882 0.813333
140 NSS 0.505882 0.694118
141 PAJ 0.505882 0.769231
142 0UM 0.505882 0.833333
143 LAD 0.505747 0.769231
144 KAA 0.505747 0.689655
145 AHX 0.5 0.779221
146 A3T 0.5 0.9375
147 62X 0.5 0.766234
148 TXA 0.5 0.786667
149 PTJ 0.5 0.734177
150 3D1 0.5 0.878788
151 ACK 0.5 0.785714
152 00A 0.5 0.74359
153 SP1 0.5 0.746667
154 3L1 0.5 0.878788
155 DLL 0.5 0.783784
156 NVA LMS 0.5 0.651685
157 RP1 0.5 0.746667
158 JB6 0.5 0.74359
159 LEU LMS 0.494253 0.651685
160 K15 0.494253 0.786667
161 3UK 0.494253 0.773333
162 OAD 0.494253 0.797297
163 9X8 0.494253 0.776316
164 ADP BMA 0.494253 0.821918
165 26A 0.492537 0.865672
166 2FA 0.492537 0.895522
167 WAQ 0.488636 0.74359
168 B5V 0.488636 0.763158
169 A A 0.488636 0.794521
170 P5A 0.488636 0.681818
171 GSU 0.488636 0.674419
172 PR8 0.488636 0.759494
173 PAP 0.4875 0.805556
174 2BA 0.486842 0.788732
175 A2P 0.486842 0.777778
176 CMP 0.486842 0.8
177 5F1 0.485294 0.80597
178 ATP A A A 0.483516 0.805556
179 YAP 0.483516 0.753247
180 ATP A 0.483516 0.805556
181 NB8 0.483146 0.75641
182 ME8 0.483146 0.707317
183 SXZ 0.483146 0.773333
184 9K8 0.483146 0.651685
185 3OD 0.483146 0.797297
186 BIS 0.483146 0.766234
187 FYA 0.483146 0.783784
188 1ZZ 0.483146 0.707317
189 7MD 0.478723 0.772152
190 XAH 0.478261 0.75
191 YSA 0.478261 0.674419
192 B1U 0.478261 0.637363
193 KB1 0.477778 0.808219
194 MYR AMP 0.477778 0.707317
195 25L 0.477778 0.808219
196 MTP 0.477612 0.826087
197 V3L 0.47561 0.794521
198 7D3 0.473684 0.76
199 9SN 0.472527 0.734177
200 6MD 0.470588 0.921875
201 1DA 0.470588 0.967742
202 PPS 0.46988 0.716049
203 NOC 0.469697 0.873016
204 FA5 0.467391 0.763158
205 B5M 0.467391 0.753247
206 B5Y 0.467391 0.753247
207 8PZ 0.467391 0.694118
208 D3Y 0.465116 0.895522
209 AR6 AR6 0.463158 0.794521
210 2VA 0.4625 0.909091
211 GTA 0.458333 0.728395
212 TYR AMP 0.457447 0.753247
213 4UV 0.457447 0.753247
214 AMP DBH 0.457447 0.797297
215 2A5 0.45679 0.773333
216 7C5 0.452632 0.794521
217 G3A 0.452632 0.75641
218 ATR 0.451219 0.791667
219 NVA 2AD 0.451219 0.857143
220 7D4 0.45 0.76
221 5NB 0.449275 0.910448
222 ARJ 0.449275 0.828125
223 4UU 0.447917 0.753247
224 ARG AMP 0.447917 0.740741
225 G5P 0.447917 0.75641
226 AFH 0.447917 0.769231
227 GA7 0.447917 0.810811
228 VRT 0.445783 0.869565
229 SO8 0.445783 0.895522
230 6V0 0.444444 0.779221
231 DQV 0.443299 0.808219
232 TAD 0.443299 0.746835
233 4YB 0.443299 0.659091
234 KH3 0.443299 0.8
235 N37 0.44 0.802817
236 ERJ 0.44 0.890625
237 3NZ 0.43956 0.857143
238 AHZ 0.438776 0.707317
239 HZ2 0.438776 0.847222
240 LAQ 0.438776 0.707317
241 A2R 0.436782 0.808219
242 7MC 0.435644 0.753086
243 YLC 0.435644 0.75
244 OZP 0.434343 0.819444
245 LPA AMP 0.434343 0.707317
246 KOY 0.434343 0.828571
247 YLP 0.434343 0.731707
248 48N 0.434343 0.75641
249 101 0.434211 0.756757
250 NAX 0.43 0.7375
251 HY8 0.43 0.847222
252 UP5 0.43 0.776316
253 NXX 0.43 0.786667
254 DND 0.43 0.786667
255 4UW 0.43 0.725
256 TXD 0.43 0.789474
257 NAI 0.43 0.766234
258 A A A 0.428571 0.783784
259 AFX 0.428571 0.742857
260 PO4 PO4 A A A A PO4 0.428571 0.777778
261 IOT 0.427184 0.722892
262 TXE 0.425743 0.789474
263 AF3 ADP 3PG 0.425743 0.725
264 TYM 0.425743 0.763158
265 WSA 0.425743 0.682353
266 649 0.425743 0.644444
267 OMR 0.425743 0.719512
268 J4G 0.423913 0.753247
269 UPA 0.421569 0.789474
270 F0P 0.421569 0.819444
271 YLB 0.421569 0.731707
272 AP0 0.421569 0.75641
273 4TC 0.421569 0.75641
274 8Q2 0.421569 0.670455
275 CNA 0.419048 0.786667
276 A4P 0.417476 0.73494
277 6CR 0.416667 0.882353
278 5J9 0.414894 0.773333
279 AV2 0.413793 0.746667
280 V1N 0.412371 0.794521
281 NAD 0.411215 0.783784
282 D5M 0.410256 0.733333
283 DA 0.410256 0.733333
284 139 0.409524 0.759494
285 ADJ 0.409524 0.740741
286 T5A 0.409524 0.710843
287 YLA 0.409524 0.731707
288 J1D 0.407407 0.642105
289 IVH 0.407407 0.810811
290 DZD 0.407407 0.769231
291 3AT 0.406977 0.794521
292 BS5 0.40566 0.693182
293 AYB 0.40566 0.722892
294 IMO 0.405063 0.753425
295 AS 0.405063 0.696203
296 0XU 0.404762 0.823529
297 AD3 0.402778 0.967742
298 LQJ 0.402062 0.794521
299 F2R 0.401869 0.753086
300 EO7 0.4 0.682353
301 6MZ 0.4 0.780822
302 GGZ 0.4 0.691358
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C9V; Ligand: ERS; Similar sites found with APoc: 17
This union binding pocket(no: 1) in the query (biounit: 6c9v.bio1) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 2VAR AMP 6.70927
2 2VAR AMP 6.70927
3 2VAR AMP 6.70927
4 2VAR ANP 6.70927
5 2VAR ANP 6.70927
6 2VAR ANP 6.70927
7 6ILS ATP 8.6262
8 6ILS ATP 8.6262
9 2HW1 FRU 8.72483
10 6A8A ATP 32.4074
11 6A8A ATP 32.4074
12 1V1A ADP 36.8932
13 4XDA ADP 39.1586
14 4XDA ADP 39.1586
15 2C49 ANP 43.0464
16 2C49 ADN 43.0464
17 2C49 ANP 43.0464
Pocket No.: 2; Query (leader) PDB : 6C9V; Ligand: ERS; Similar sites found with APoc: 17
This union binding pocket(no: 2) in the query (biounit: 6c9v.bio1) has 70 residues
No: Leader PDB Ligand Sequence Similarity
1 2VAR AMP 6.70927
2 2VAR AMP 6.70927
3 2VAR AMP 6.70927
4 2VAR ANP 6.70927
5 2VAR ANP 6.70927
6 2VAR ANP 6.70927
7 6ILS ATP 8.6262
8 6ILS ATP 8.6262
9 2HW1 FRU 8.72483
10 6A8A ATP 32.4074
11 6A8A ATP 32.4074
12 1V1A ADP 36.8932
13 4XDA ADP 39.1586
14 4XDA ADP 39.1586
15 2C49 ANP 43.0464
16 2C49 ADN 43.0464
17 2C49 ANP 43.0464
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