Receptor
PDB id Resolution Class Description Source Keywords
2PKM 1.9 Å EC: 2.7.1.20 CRYSTAL STRUCTURE OF M TUBERCULOSIS ADENOSINE KINASE COMPLEX ADENOSINE MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE ADENOSINE TRASTRUCTURAL GENOMICS TB STRUCTURAL GENOMICS CONSORTIUM TBS
Ref.: HIGH RESOLUTION CRYSTAL STRUCTURES OF MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE: INSIGHTS INTO THE ME AND SPECIFICITY OF THIS NOVEL PROKARYOTIC ENZYME J.BIOL.CHEM. V. 282 27334 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ADN A:501;
Valid;
none;
submit data
267.241 C10 H13 N5 O4 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: ADN; Similar ligands found: 331
No: Ligand ECFP6 Tc MDL keys Tc
1 XYA 1 1
2 ADN 1 1
3 RAB 1 1
4 5N5 0.811321 0.967742
5 5CD 0.796296 0.920635
6 A4D 0.796296 0.967742
7 MTA 0.758621 0.878788
8 EP4 0.754386 0.852941
9 M2T 0.741379 0.828571
10 DTA 0.741379 0.865672
11 AMP 0.709677 0.842857
12 A 0.709677 0.842857
13 3DH 0.704918 0.878788
14 LMS 0.68254 0.7375
15 ZAS 0.68254 0.84058
16 5AD 0.672727 0.854839
17 SRA 0.671875 0.797297
18 6RE 0.671875 0.830986
19 DSH 0.661538 0.842857
20 AOC 0.661538 0.907692
21 7D7 0.660714 0.875
22 45A 0.651515 0.819444
23 ABM 0.651515 0.819444
24 A3N 0.651515 0.923077
25 A2D 0.651515 0.84507
26 J7C 0.651515 0.842857
27 ADP 0.647059 0.84507
28 S4M 0.641791 0.766234
29 GJV 0.641791 0.819444
30 3AM 0.640625 0.828571
31 AN2 0.637681 0.833333
32 BA3 0.632353 0.84507
33 A12 0.632353 0.810811
34 MAO 0.632353 0.75641
35 AP2 0.632353 0.810811
36 Y3J 0.627119 0.828125
37 5AS 0.623188 0.714286
38 B4P 0.623188 0.84507
39 AP5 0.623188 0.84507
40 5X8 0.619718 0.865672
41 HEJ 0.619718 0.84507
42 ATP 0.619718 0.84507
43 SON 0.614286 0.786667
44 AT4 0.614286 0.810811
45 ADP MG 0.614286 0.842857
46 A7D 0.614286 0.909091
47 AQP 0.611111 0.84507
48 APC 0.611111 0.810811
49 5FA 0.611111 0.84507
50 2FA 0.606557 0.924242
51 26A 0.606557 0.893939
52 MHZ 0.605634 0.75641
53 M33 0.605634 0.833333
54 CA0 0.605634 0.821918
55 ADX 0.605634 0.759494
56 AU1 0.605634 0.821918
57 AD9 0.60274 0.821918
58 AGS 0.60274 0.8
59 SAP 0.60274 0.8
60 2AM 0.6 0.842857
61 SFG 0.597222 0.850746
62 ACP 0.597222 0.821918
63 50T 0.597222 0.833333
64 H1Q 0.597222 0.830986
65 KG4 0.597222 0.821918
66 MTP 0.590164 0.852941
67 APR 0.589041 0.84507
68 AR6 0.589041 0.84507
69 PRX 0.589041 0.797297
70 A3G 0.588235 0.938462
71 ACQ 0.586667 0.821918
72 TAT 0.586667 0.810811
73 T99 0.586667 0.810811
74 A3P 0.585714 0.816901
75 SA8 0.581081 0.794521
76 ADP PO3 0.581081 0.842857
77 ATP MG 0.581081 0.842857
78 RBY 0.581081 0.810811
79 APC MG 0.581081 0.819444
80 ADV 0.581081 0.810811
81 A5D 0.581081 0.865672
82 6MD 0.580645 0.952381
83 1DA 0.580645 1
84 ADQ 0.575 0.847222
85 OVE 0.573529 0.808219
86 SAH 0.573333 0.84058
87 SAI 0.573333 0.828571
88 G5A 0.573333 0.714286
89 A22 0.56962 0.833333
90 ANP 0.565789 0.821918
91 GAP 0.565789 0.821918
92 SAM 0.565789 0.773333
93 NEC 0.565217 0.876923
94 3AD 0.564516 0.951613
95 6YZ 0.564103 0.821918
96 25A 0.5625 0.819444
97 7D5 0.560606 0.780822
98 8LE 0.558442 0.776316
99 5AL 0.558442 0.808219
100 AAT 0.558442 0.819444
101 EEM 0.558442 0.773333
102 HQG 0.556962 0.833333
103 ALF ADP 0.551282 0.776316
104 A5A 0.551282 0.719512
105 ADP ALF 0.551282 0.776316
106 ATF 0.551282 0.810811
107 CC5 0.55 0.935484
108 A3S 0.547945 0.953125
109 SMM 0.544304 0.74359
110 ADP VO4 0.544304 0.808219
111 SRP 0.544304 0.810811
112 SSA 0.544304 0.73494
113 S7M 0.544304 0.773333
114 8LH 0.544304 0.810811
115 VO4 ADP 0.544304 0.808219
116 QQX 0.544118 0.756757
117 S8M 0.54321 0.805556
118 N5O 0.542857 0.893939
119 ADP BMA 0.542169 0.847222
120 A2P 0.541667 0.802817
121 3D1 0.539683 0.907692
122 3L1 0.539683 0.907692
123 PAP 0.539474 0.830986
124 VMS 0.5375 0.702381
125 54H 0.5375 0.702381
126 52H 0.5375 0.694118
127 LSS 0.536585 0.678161
128 QQY 0.536232 0.767123
129 ERJ 0.536232 0.920635
130 ACK 0.536232 0.811594
131 A3T 0.533333 0.968254
132 DAL AMP 0.530864 0.808219
133 8X1 0.530864 0.689655
134 MAP 0.530864 0.8
135 5CA 0.530864 0.73494
136 TSB 0.530864 0.731707
137 8LQ 0.530864 0.786667
138 53H 0.530864 0.694118
139 N5A 0.527778 0.863636
140 OZV 0.52439 0.84507
141 5SV 0.52439 0.75641
142 8QN 0.52439 0.808219
143 GEK 0.52439 0.805556
144 9ZA 0.52439 0.766234
145 9ZD 0.52439 0.766234
146 OOB 0.52439 0.808219
147 9X8 0.52381 0.8
148 OAD 0.52381 0.821918
149 25L 0.523256 0.833333
150 PPS 0.518987 0.7375
151 DSZ 0.518072 0.714286
152 NSS 0.518072 0.714286
153 0UM 0.518072 0.808219
154 4AD 0.518072 0.8
155 AMO 0.518072 0.810811
156 A3R 0.518072 0.813333
157 PAJ 0.518072 0.792208
158 A1R 0.518072 0.813333
159 A A 0.517647 0.819444
160 6CR 0.515152 0.910448
161 RP1 0.514286 0.77027
162 SP1 0.514286 0.77027
163 2VA 0.513158 0.938462
164 NVA LMS 0.511905 0.670455
165 62X 0.511905 0.74359
166 DLL 0.511905 0.808219
167 00A 0.511905 0.766234
168 AHX 0.511905 0.802632
169 3OD 0.511628 0.821918
170 ME8 0.511628 0.728395
171 PTJ 0.511628 0.75641
172 HZ2 0.51087 0.847222
173 7D3 0.506849 0.783784
174 V3L 0.506329 0.819444
175 A6D 0.505882 0.763158
176 LEU LMS 0.505882 0.670455
177 K15 0.505882 0.763158
178 3UK 0.505882 0.797297
179 B5V 0.5 0.786667
180 ATR 0.5 0.816901
181 5F1 0.5 0.80597
182 WAQ 0.5 0.766234
183 CMP 0.5 0.826087
184 HY8 0.5 0.847222
185 NVA 2AD 0.5 0.884058
186 LAD 0.5 0.769231
187 KAA 0.5 0.689655
188 2BA 0.5 0.814286
189 AD3 0.5 1
190 P5A 0.5 0.681818
191 PR8 0.5 0.759494
192 GSU 0.5 0.694118
193 ATP A A A 0.494382 0.830986
194 ATP A 0.494382 0.830986
195 FYA 0.494253 0.808219
196 JB6 0.494253 0.766234
197 1ZZ 0.494253 0.728395
198 SXZ 0.494253 0.773333
199 9K8 0.494253 0.670455
200 NB8 0.494253 0.779221
201 BIS 0.494253 0.789474
202 TXA 0.494253 0.810811
203 SO8 0.493671 0.924242
204 VRT 0.493671 0.897059
205 IVH 0.493333 0.835616
206 KB1 0.488636 0.783784
207 MYR AMP 0.488636 0.728395
208 2A5 0.487179 0.797297
209 NOC 0.484375 0.903226
210 4UV 0.483516 0.776316
211 9SN 0.483146 0.75641
212 A2R 0.481928 0.833333
213 7D4 0.480519 0.783784
214 B5Y 0.477778 0.776316
215 YAP 0.477778 0.776316
216 B5M 0.477778 0.776316
217 8PZ 0.477778 0.714286
218 FA5 0.477778 0.786667
219 D3Y 0.47619 0.924242
220 AR6 AR6 0.473118 0.819444
221 AFH 0.473118 0.792208
222 XAH 0.472527 0.75
223 YSA 0.472527 0.694118
224 B1U 0.472527 0.655556
225 EKK 0.469697 0.923077
226 3BH 0.46875 0.953125
227 TBN 0.46875 0.983607
228 AMP DBH 0.467391 0.821918
229 TYR AMP 0.467391 0.776316
230 101 0.465753 0.780822
231 LAQ 0.463158 0.728395
232 TO1 0.462687 0.952381
233 G3A 0.462366 0.779221
234 7C5 0.462366 0.819444
235 ERS 0.461538 0.855072
236 UPA 0.459184 0.813333
237 LPA AMP 0.458333 0.728395
238 GA7 0.457447 0.835616
239 G5P 0.457447 0.779221
240 ARG AMP 0.457447 0.740741
241 7MD 0.457447 0.772152
242 4UU 0.457447 0.776316
243 ERP 0.455696 0.90625
244 5ID 0.454545 0.923077
245 A A A 0.454545 0.808219
246 EKH 0.454545 0.923077
247 DQV 0.452632 0.833333
248 GTA 0.452632 0.75
249 TAD 0.452632 0.769231
250 KH3 0.452632 0.776316
251 4YB 0.452632 0.678161
252 J4G 0.449438 0.776316
253 3NZ 0.449438 0.884058
254 TYM 0.44898 0.786667
255 WSA 0.44898 0.702381
256 OMR 0.44898 0.740741
257 AHZ 0.447917 0.728395
258 FTU 0.447761 0.923077
259 139 0.445545 0.782051
260 KOY 0.443299 0.855072
261 YLP 0.443299 0.731707
262 48N 0.443299 0.779221
263 OZP 0.443299 0.794521
264 AFX 0.441176 0.768116
265 ARJ 0.441176 0.857143
266 LQJ 0.44086 0.819444
267 AV2 0.440476 0.77027
268 DA 0.44 0.756757
269 D5M 0.44 0.756757
270 5J9 0.43956 0.773333
271 NXX 0.438776 0.810811
272 UP5 0.438776 0.8
273 6V0 0.438776 0.779221
274 NAI 0.438776 0.789474
275 NAX 0.438776 0.759494
276 4UW 0.438776 0.746835
277 DND 0.438776 0.810811
278 TXD 0.438776 0.789474
279 PO4 PO4 A A A A PO4 0.438202 0.802817
280 NA7 0.438202 0.810811
281 MZR 0.4375 0.859375
282 V1N 0.43617 0.819444
283 HO4 0.434783 0.952381
284 649 0.434343 0.662921
285 AF3 ADP 3PG 0.434343 0.746835
286 N37 0.434343 0.802817
287 TXE 0.434343 0.789474
288 IMO 0.434211 0.777778
289 3AT 0.433735 0.819444
290 G A A A 0.432692 0.779221
291 4TC 0.43 0.779221
292 AP0 0.43 0.779221
293 8Q2 0.43 0.689655
294 7MC 0.43 0.753086
295 YLB 0.43 0.731707
296 YLC 0.43 0.75
297 F0P 0.43 0.794521
298 6MZ 0.428571 0.805556
299 SGV 0.428571 0.967742
300 BS5 0.427184 0.674157
301 A4P 0.425743 0.73494
302 IOT 0.421569 0.722892
303 DAT 0.419753 0.76
304 COD 0.419048 0.72619
305 YLA 0.417476 0.731707
306 ADJ 0.417476 0.740741
307 T5A 0.417476 0.731707
308 AS 0.415584 0.717949
309 J1D 0.415094 0.625
310 0XU 0.414634 0.823529
311 CNA 0.413462 0.810811
312 AYB 0.413462 0.722892
313 103 0.413333 0.716216
314 A U 0.411765 0.8
315 80F 0.411215 0.731707
316 GMP 0.410959 0.882353
317 EO7 0.410256 0.702381
318 F2R 0.409524 0.753086
319 GGZ 0.409091 0.7125
320 U A 0.407407 0.766234
321 ITT 0.407407 0.791667
322 AMP NAD 0.40566 0.808219
323 A G 0.40566 0.766234
324 BTX 0.40566 0.710843
325 4TA 0.40566 0.719512
326 NAD 0.40566 0.808219
327 SFB 0.401961 0.709302
328 BT5 0.401869 0.702381
329 DZD 0.401869 0.769231
330 U A G G 0.401869 0.766234
331 DTP 0.4 0.76
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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