Receptor
PDB id Resolution Class Description Source Keywords
3V80 2.03 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH 5'-O-PROPARGYLAMINO-5'-DEOXYADENOSINE LISTERIA MONOCYTOGENES LIGAND-SCREENING BY CRYSTALLOGRAPHY TWO-DOMAIN KINASE INORPOLYPHOSPHATE/ATP-NAD KINASE 1 TRANSFERASE
Ref.: SCREENING AND IN SITU SYNTHESIS USING CRYSTALS OF A KINASE LEAD TO A POTENT ANTISTAPHYLOCOCCAL COMPOUND STRUCTURE V. 20 1107 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AOC A:301;
A:302;
Valid;
Valid;
none;
none;
submit data
305.289 C13 H15 N5 O4 C#CCO...
CIT A:303;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
GOL A:304;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DHU 2.33 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH A NOVEL INHIBITOR LISTERIA MONOCYTOGENES SEROVAR 1/2A (SATCC BAA-679 / EGD-E) TETRAMERIC NAD KINASE TRANSFERASE
Ref.: 8-THIOALKYL-ADENOSINE DERIVATIVES INHIBIT LISTERIA MONOCYTOGENES NAD KINASE THROUGH A NOVEL BINDING MO EUR.J.MED.CHEM. V. 124 1041 2016
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AOC; Similar ligands found: 301
No: Ligand ECFP6 Tc MDL keys Tc
1 AOC 1 1
2 LMS 0.666667 0.740741
3 A 0.666667 0.84507
4 AMP 0.666667 0.84507
5 RAB 0.661538 0.907692
6 ADN 0.661538 0.907692
7 XYA 0.661538 0.907692
8 SRA 0.657534 0.8
9 SON 0.649351 0.789474
10 5N5 0.641791 0.878788
11 A3N 0.64 0.924242
12 45A 0.64 0.821918
13 ABM 0.64 0.821918
14 A2D 0.64 0.821918
15 5CD 0.632353 0.892308
16 A4D 0.632353 0.878788
17 AP2 0.623377 0.789474
18 A12 0.623377 0.789474
19 BA3 0.623377 0.821918
20 AU1 0.620253 0.8
21 AP5 0.615385 0.821918
22 5AS 0.615385 0.697674
23 ADP 0.615385 0.821918
24 B4P 0.615385 0.821918
25 H1Q 0.6125 0.833333
26 ADP MG 0.607595 0.84507
27 AN2 0.607595 0.810811
28 AT4 0.607595 0.789474
29 EP4 0.605634 0.855072
30 M33 0.6 0.810811
31 ADX 0.6 0.740741
32 CA0 0.6 0.8
33 DTA 0.597222 0.84058
34 M2T 0.597222 0.830986
35 3DH 0.594595 0.880597
36 ACP 0.592593 0.8
37 ATP 0.592593 0.821918
38 50T 0.592593 0.810811
39 KG4 0.592593 0.8
40 HEJ 0.592593 0.821918
41 MTA 0.589041 0.880597
42 AR6 0.585366 0.821918
43 5FA 0.585366 0.821918
44 PRX 0.585366 0.8
45 APC 0.585366 0.789474
46 AQP 0.585366 0.821918
47 APR 0.585366 0.821918
48 SAP 0.578313 0.779221
49 RBY 0.578313 0.789474
50 AGS 0.578313 0.779221
51 AD9 0.578313 0.8
52 ATP MG 0.578313 0.84507
53 ADP PO3 0.578313 0.84507
54 APC MG 0.578313 0.821918
55 ADV 0.578313 0.789474
56 G5A 0.571429 0.697674
57 ALF ADP 0.569767 0.779221
58 ADP ALF 0.569767 0.779221
59 GAP 0.564706 0.8
60 T99 0.564706 0.789474
61 ACQ 0.564706 0.8
62 ANP 0.564706 0.8
63 TAT 0.564706 0.789474
64 OOB 0.561798 0.810811
65 5AD 0.558824 0.828125
66 ZAS 0.558442 0.816901
67 8LE 0.55814 0.779221
68 5AL 0.55814 0.810811
69 ATF 0.551724 0.789474
70 A5A 0.551724 0.722892
71 6RE 0.551282 0.783784
72 8LQ 0.550562 0.789474
73 DAL AMP 0.550562 0.810811
74 8X1 0.550562 0.674157
75 VO4 ADP 0.545455 0.810811
76 SSA 0.545455 0.697674
77 8LH 0.545455 0.789474
78 6YZ 0.545455 0.8
79 ADP VO4 0.545455 0.810811
80 SRP 0.545455 0.789474
81 5SV 0.544444 0.759494
82 DSH 0.544304 0.819444
83 MAO 0.54321 0.782051
84 VMS 0.539326 0.705882
85 54H 0.539326 0.705882
86 52H 0.539326 0.697674
87 HQG 0.539326 0.810811
88 PAJ 0.538462 0.75
89 ADQ 0.538462 0.8
90 B5V 0.537634 0.789474
91 J7C 0.5375 0.794521
92 TSB 0.533333 0.714286
93 53H 0.533333 0.697674
94 MAP 0.533333 0.779221
95 5CA 0.533333 0.697674
96 A22 0.533333 0.810811
97 DLL 0.532609 0.810811
98 00A 0.532609 0.769231
99 1ZZ 0.531915 0.731707
100 S4M 0.530864 0.746835
101 GJV 0.530864 0.773333
102 7D7 0.528571 0.820895
103 25A 0.527473 0.821918
104 OZV 0.527473 0.821918
105 9ZD 0.527473 0.769231
106 8QN 0.527473 0.810811
107 9ZA 0.527473 0.769231
108 ADP BMA 0.526882 0.8
109 3UK 0.526882 0.8
110 MYR AMP 0.526316 0.731707
111 AMO 0.521739 0.789474
112 DSZ 0.521739 0.697674
113 LSS 0.521739 0.681818
114 4AD 0.521739 0.779221
115 A3R 0.521739 0.769231
116 NSS 0.521739 0.697674
117 A1R 0.521739 0.769231
118 P5A 0.521277 0.666667
119 WAQ 0.521277 0.769231
120 GSU 0.521277 0.697674
121 A A 0.521277 0.821918
122 AMP DBH 0.520408 0.8
123 SFG 0.517647 0.826087
124 5X8 0.517647 0.867647
125 NVA LMS 0.516129 0.674157
126 AHX 0.516129 0.759494
127 3OD 0.515789 0.8
128 PTJ 0.515789 0.759494
129 9K8 0.515789 0.674157
130 FYA 0.515789 0.810811
131 7C5 0.515152 0.821918
132 A7D 0.511905 0.882353
133 9X8 0.510638 0.779221
134 OAD 0.510638 0.8
135 LEU LMS 0.510638 0.674157
136 8Q2 0.509615 0.712644
137 Y3J 0.506849 0.80303
138 3AM 0.506329 0.805556
139 MHZ 0.505882 0.7375
140 A5D 0.505747 0.84058
141 KAA 0.505263 0.674157
142 LAD 0.505263 0.75
143 PR8 0.505263 0.740741
144 9SN 0.505155 0.759494
145 B5M 0.5 0.779221
146 B5Y 0.5 0.779221
147 ATP A 0.5 0.833333
148 JB6 0.5 0.769231
149 FA5 0.5 0.789474
150 BIS 0.5 0.769231
151 ME8 0.5 0.753086
152 TXA 0.5 0.789474
153 ATP A A A 0.5 0.833333
154 NB8 0.5 0.759494
155 YAP 0.5 0.779221
156 8PZ 0.5 0.697674
157 YLA 0.495327 0.756098
158 YSA 0.494949 0.697674
159 B1U 0.494949 0.659341
160 25L 0.494845 0.810811
161 4YB 0.490196 0.681818
162 TYR AMP 0.49 0.779221
163 AAT 0.488889 0.797297
164 SA8 0.488636 0.797297
165 A3P 0.488095 0.819444
166 SAI 0.483146 0.830986
167 SAH 0.483146 0.842857
168 7D5 0.481013 0.76
169 KOY 0.480769 0.857143
170 AFH 0.480392 0.75
171 7MD 0.480392 0.731707
172 XAH 0.48 0.731707
173 SMM 0.478261 0.769231
174 SAM 0.477778 0.776316
175 NAI 0.47619 0.792208
176 NXX 0.47619 0.789474
177 DND 0.47619 0.789474
178 DQV 0.475728 0.810811
179 4UV 0.475248 0.802632
180 2AM 0.475 0.794521
181 EEM 0.472527 0.776316
182 OMR 0.471698 0.722892
183 649 0.471698 0.666667
184 LAQ 0.471154 0.731707
185 AHZ 0.471154 0.731707
186 G3A 0.470588 0.759494
187 A2P 0.470588 0.805556
188 A3G 0.46988 0.855072
189 NEC 0.46988 0.797101
190 LPA AMP 0.466667 0.731707
191 4UU 0.466019 0.802632
192 GA7 0.466019 0.789474
193 ARG AMP 0.466019 0.722892
194 AR6 AR6 0.466019 0.821918
195 G5P 0.466019 0.759494
196 CC5 0.465753 0.90625
197 S7M 0.462366 0.776316
198 TAD 0.461538 0.75
199 GTA 0.461538 0.731707
200 3AD 0.460526 0.892308
201 0UM 0.458333 0.763158
202 WSA 0.457944 0.705882
203 AF3 ADP 3PG 0.457944 0.75
204 TXE 0.457944 0.792208
205 TYM 0.457944 0.789474
206 OVE 0.457831 0.763158
207 PAP 0.455556 0.808219
208 YLB 0.453704 0.714286
209 7MC 0.453704 0.714286
210 YLP 0.45283 0.714286
211 48N 0.45283 0.759494
212 N5O 0.452381 0.814286
213 K15 0.44898 0.766234
214 A6D 0.44898 0.74359
215 TXD 0.448598 0.815789
216 6V0 0.448598 0.782051
217 4UW 0.448598 0.772152
218 NAX 0.448598 0.7625
219 UP5 0.448598 0.802632
220 S8M 0.447917 0.808219
221 GEK 0.447917 0.808219
222 QQY 0.445783 0.723684
223 V3L 0.445652 0.821918
224 2A5 0.444444 0.753247
225 SLU 0.443478 0.689655
226 A3S 0.443182 0.867647
227 NAD 0.442478 0.810811
228 7D3 0.44186 0.74026
229 N5A 0.44186 0.785714
230 T5A 0.441441 0.73494
231 PPS 0.44086 0.719512
232 AP0 0.440367 0.782051
233 UPA 0.440367 0.792208
234 4TC 0.440367 0.782051
235 YLC 0.440367 0.753086
236 ATR 0.43956 0.794521
237 62X 0.438776 0.746835
238 DZD 0.438596 0.772152
239 7D4 0.438202 0.74026
240 CNA 0.4375 0.789474
241 A4P 0.436364 0.717647
242 KB1 0.435644 0.786667
243 A3D 0.434783 0.8
244 QQX 0.433735 0.714286
245 A3T 0.433333 0.880597
246 IOT 0.432432 0.705882
247 IMO 0.430233 0.780822
248 J4G 0.43 0.779221
249 COD 0.429825 0.689655
250 4TA 0.429825 0.743902
251 G A A A 0.429825 0.759494
252 AMP NAD 0.429825 0.810811
253 SP1 0.428571 0.75
254 139 0.428571 0.7625
255 ADJ 0.428571 0.765432
256 RP1 0.428571 0.75
257 ACK 0.428571 0.763889
258 NO7 0.427083 0.813333
259 A2R 0.427083 0.810811
260 BT5 0.426087 0.705882
261 SXZ 0.425743 0.776316
262 6MZ 0.425287 0.808219
263 EO7 0.425287 0.705882
264 AYB 0.424779 0.705882
265 M24 0.423729 0.740741
266 3L1 0.423077 0.826087
267 MTP 0.423077 0.777778
268 3D1 0.423077 0.826087
269 80F 0.422414 0.73494
270 F2R 0.421053 0.714286
271 2BA 0.420455 0.791667
272 CMP 0.420455 0.802817
273 NAE 0.420168 0.779221
274 A A A 0.42 0.810811
275 PO4 PO4 A A A A PO4 0.42 0.805556
276 NAJ PZO 0.418803 0.782051
277 N37 0.418182 0.830986
278 26A 0.417722 0.84058
279 2FA 0.417722 0.842857
280 2VA 0.417582 0.855072
281 BTX 0.417391 0.714286
282 A G 0.417391 0.769231
283 NAQ 0.416667 0.759494
284 U A G G 0.413793 0.769231
285 ZID 0.413223 0.8
286 5F1 0.4125 0.782609
287 YLY 0.411765 0.705882
288 D3Y 0.408163 0.842857
289 KH3 0.407407 0.75641
290 U A 0.40678 0.792208
291 ITT 0.406593 0.77027
292 PGS 0.406593 0.725
293 NA7 0.405941 0.789474
294 NDE 0.404762 0.789474
295 SO8 0.404255 0.842857
296 3NZ 0.401961 0.833333
297 F0P 0.401786 0.797297
298 3AT 0.4 0.797297
299 1DA 0.4 0.907692
300 6MD 0.4 0.865672
301 OZP 0.4 0.797297
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DHU; Ligand: 5A8; 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: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DHU; Ligand: 5A8; 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: 5dhu.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5dhu.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
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