Receptor
PDB id Resolution Class Description Source Keywords
3V7U 1.97 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH MTA 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
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...
MTA A:301;
A:302;
Valid;
Valid;
none;
none;
submit data
297.334 C11 H15 N5 O3 S CSC[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: MTA; Similar ligands found: 290
No: Ligand ECFP6 Tc MDL keys Tc
1 MTA 1 1
2 DTA 0.786885 0.867647
3 3DH 0.777778 0.938462
4 ADN 0.758621 0.878788
5 XYA 0.758621 0.878788
6 RAB 0.758621 0.878788
7 DSH 0.705882 0.84507
8 5N5 0.704918 0.878788
9 5CD 0.693548 0.892308
10 A4D 0.693548 0.907692
11 EP4 0.6875 0.939394
12 M2T 0.676923 0.940298
13 A7D 0.657534 0.882353
14 5X8 0.64 0.895522
15 5AD 0.639344 0.857143
16 ZAS 0.628571 0.816901
17 LMS 0.628571 0.719512
18 AMP 0.628571 0.794521
19 A 0.628571 0.794521
20 A5D 0.623377 0.867647
21 SAH 0.615385 0.869565
22 J7C 0.60274 0.794521
23 ABM 0.60274 0.821918
24 45A 0.60274 0.821918
25 AAT 0.6 0.797297
26 6RE 0.597222 0.783784
27 SRA 0.597222 0.776316
28 S4M 0.594595 0.84
29 AOC 0.589041 0.880597
30 MAO 0.586667 0.805195
31 S8M 0.583333 0.833333
32 A2D 0.581081 0.773333
33 A3N 0.581081 0.867647
34 5AS 0.578947 0.697674
35 GJV 0.573333 0.773333
36 A12 0.565789 0.74359
37 AP2 0.565789 0.74359
38 BA3 0.565789 0.773333
39 M33 0.564103 0.810811
40 ADX 0.564103 0.719512
41 AU1 0.564103 0.753247
42 MHZ 0.564103 0.805195
43 AP5 0.558442 0.773333
44 ADP 0.558442 0.773333
45 B4P 0.558442 0.773333
46 7D7 0.553846 0.794118
47 Y3J 0.552239 0.80303
48 ADP MG 0.551282 0.794521
49 AT4 0.551282 0.766234
50 AN2 0.551282 0.763158
51 SON 0.551282 0.74359
52 SXZ 0.550562 0.849315
53 PRX 0.55 0.8
54 A6D 0.545455 0.766234
55 CA0 0.544304 0.753247
56 SA8 0.54321 0.873239
57 AD9 0.54321 0.753247
58 EEM 0.542169 0.849315
59 HEJ 0.5375 0.773333
60 SFG 0.5375 0.826087
61 ACP 0.5375 0.753247
62 KG4 0.5375 0.753247
63 50T 0.5375 0.763158
64 H1Q 0.5375 0.783784
65 ATP 0.5375 0.773333
66 AQP 0.530864 0.773333
67 APR 0.530864 0.773333
68 APC 0.530864 0.74359
69 AR6 0.530864 0.773333
70 5FA 0.530864 0.773333
71 SAM 0.53012 0.875
72 ANP 0.53012 0.753247
73 SMM 0.529412 0.84
74 3AM 0.527027 0.756757
75 NEC 0.526316 0.823529
76 ADV 0.52439 0.74359
77 SAP 0.52439 0.75641
78 AGS 0.52439 0.75641
79 APC MG 0.52439 0.773333
80 ATP MG 0.52439 0.794521
81 ADP PO3 0.52439 0.794521
82 RBY 0.52439 0.74359
83 8LE 0.52381 0.75641
84 5AL 0.52381 0.786667
85 54H 0.523256 0.705882
86 VMS 0.523256 0.705882
87 3AD 0.521739 0.863636
88 MTH 0.520548 0.984127
89 SAI 0.518072 0.830986
90 G5A 0.518072 0.678161
91 A5A 0.517647 0.722892
92 ME8 0.516484 0.797468
93 GAP 0.511905 0.753247
94 T99 0.511905 0.766234
95 TAT 0.511905 0.766234
96 ACQ 0.511905 0.753247
97 8LH 0.511628 0.789474
98 S7M 0.511628 0.824324
99 9ZA 0.511364 0.769231
100 9ZD 0.511364 0.769231
101 8QN 0.511364 0.786667
102 CC5 0.507463 0.876923
103 A3G 0.506494 0.828571
104 A3P 0.506329 0.77027
105 HQG 0.505747 0.763158
106 52H 0.505747 0.697674
107 NVA LMS 0.5 0.693182
108 8LQ 0.5 0.789474
109 MAP 0.5 0.734177
110 TSB 0.5 0.714286
111 53H 0.5 0.697674
112 ALF ADP 0.5 0.734177
113 DAL AMP 0.5 0.786667
114 8X1 0.5 0.655556
115 7D5 0.5 0.714286
116 ADP ALF 0.5 0.734177
117 ATF 0.5 0.74359
118 MTP 0.5 0.828571
119 25A 0.494382 0.773333
120 5SV 0.494382 0.759494
121 SRP 0.494253 0.74359
122 SSA 0.494253 0.678161
123 6YZ 0.494253 0.753247
124 VO4 ADP 0.494253 0.763158
125 ADP VO4 0.494253 0.763158
126 2AM 0.493333 0.746667
127 26A 0.492958 0.867647
128 0UM 0.488889 0.810811
129 ADQ 0.488889 0.753247
130 DSZ 0.488889 0.678161
131 A3R 0.488889 0.725
132 PAJ 0.488889 0.75
133 A1R 0.488889 0.725
134 LSS 0.488889 0.701149
135 N5O 0.487179 0.788732
136 3OD 0.483871 0.776316
137 62X 0.483516 0.815789
138 AHX 0.483516 0.716049
139 5CA 0.483146 0.678161
140 A22 0.483146 0.763158
141 2VA 0.481928 0.855072
142 A3T 0.481928 0.880597
143 SP1 0.480519 0.75
144 RP1 0.480519 0.75
145 3L1 0.478873 0.8
146 3D1 0.478873 0.8
147 OAD 0.478261 0.776316
148 9X8 0.478261 0.779221
149 K15 0.478261 0.813333
150 LEU LMS 0.478261 0.693182
151 GEK 0.477778 0.833333
152 OZV 0.477778 0.773333
153 OOB 0.477778 0.763158
154 A3S 0.47561 0.84058
155 N5A 0.475 0.785714
156 OVE 0.474359 0.74026
157 P5A 0.473118 0.648352
158 PR8 0.473118 0.698795
159 AMO 0.472527 0.74359
160 4AD 0.472527 0.734177
161 NSS 0.472527 0.678161
162 2FA 0.472222 0.816901
163 6MD 0.472222 0.893939
164 NOC 0.471429 0.791045
165 NVA 2AD 0.470588 0.833333
166 2BA 0.469136 0.767123
167 A2P 0.469136 0.756757
168 CMP 0.469136 0.777778
169 1ZZ 0.468085 0.731707
170 PTJ 0.468085 0.759494
171 TXA 0.468085 0.766234
172 9K8 0.468085 0.674157
173 QQX 0.467532 0.714286
174 00A 0.467391 0.725
175 DLL 0.467391 0.763158
176 5F1 0.465753 0.782609
177 MYR AMP 0.463158 0.731707
178 ADP BMA 0.462366 0.753247
179 3UK 0.462366 0.753247
180 ACK 0.461538 0.739726
181 QQY 0.461538 0.723684
182 A A 0.457447 0.773333
183 WAQ 0.457447 0.725
184 LAD 0.457447 0.707317
185 KAA 0.457447 0.655556
186 GSU 0.457447 0.678161
187 B5V 0.457447 0.74359
188 PPS 0.454545 0.698795
189 B5M 0.453608 0.75641
190 B5Y 0.453608 0.75641
191 PAP 0.453488 0.76
192 JB6 0.452632 0.746835
193 BIS 0.452632 0.725
194 FYA 0.452632 0.763158
195 NB8 0.452632 0.716049
196 1DA 0.452055 0.878788
197 XAH 0.44898 0.690476
198 VRT 0.448276 0.84507
199 SO8 0.448276 0.869565
200 25L 0.447917 0.763158
201 KB1 0.447917 0.786667
202 4UV 0.444444 0.734177
203 9SN 0.443299 0.716049
204 V3L 0.443182 0.773333
205 LAQ 0.441176 0.710843
206 7D3 0.439024 0.696203
207 ATP A A A 0.438776 0.783784
208 FA5 0.438776 0.74359
209 8PZ 0.438776 0.678161
210 ATP A 0.438776 0.783784
211 YAP 0.438776 0.734177
212 J1A 0.4375 0.740741
213 LPA AMP 0.436893 0.710843
214 J1C 0.435897 0.67033
215 GA7 0.435644 0.789474
216 4UU 0.435644 0.734177
217 AFH 0.435644 0.707317
218 7MD 0.435644 0.690476
219 J1B 0.434783 0.67033
220 B1U 0.434343 0.641304
221 YSA 0.434343 0.678161
222 TXD 0.432692 0.746835
223 4UW 0.432692 0.75
224 ARJ 0.432432 0.776119
225 MCF 0.432099 0.842857
226 GTA 0.431373 0.731707
227 4YB 0.431373 0.662921
228 TAD 0.431373 0.728395
229 KH3 0.431373 0.802632
230 AMP DBH 0.43 0.753247
231 TYR AMP 0.43 0.734177
232 IVH 0.428571 0.813333
233 AHZ 0.427184 0.731707
234 HZ2 0.427184 0.776316
235 3NZ 0.427083 0.833333
236 G3A 0.425743 0.716049
237 7C5 0.425743 0.773333
238 2A5 0.425287 0.708861
239 ERJ 0.425 0.835821
240 AP0 0.424528 0.7375
241 7MC 0.424528 0.694118
242 TT8 0.423913 0.898551
243 YLP 0.423077 0.694118
244 KOY 0.423077 0.805556
245 48N 0.423077 0.7375
246 CNA 0.422018 0.74359
247 G5P 0.421569 0.716049
248 ARG AMP 0.421569 0.682353
249 AR6 AR6 0.421569 0.773333
250 ATR 0.420455 0.746667
251 101 0.419753 0.714286
252 D3Y 0.419355 0.816901
253 NXX 0.419048 0.74359
254 NAX 0.419048 0.698795
255 NAI 0.419048 0.725
256 6V0 0.419048 0.716049
257 HY8 0.419048 0.776316
258 DND 0.419048 0.74359
259 7D4 0.418605 0.696203
260 DQV 0.417476 0.763158
261 A A A 0.416667 0.763158
262 TXE 0.415094 0.725
263 649 0.415094 0.648352
264 OMR 0.415094 0.722892
265 DA 0.414634 0.714286
266 D5M 0.414634 0.714286
267 T5A 0.412844 0.694118
268 139 0.412844 0.698795
269 ADJ 0.412844 0.702381
270 J4G 0.412371 0.734177
271 F0P 0.411215 0.797297
272 YLC 0.411215 0.710843
273 8Q2 0.411215 0.655556
274 YLB 0.411215 0.714286
275 J1D 0.410714 0.628866
276 OZP 0.409524 0.797297
277 AYB 0.409091 0.705882
278 A2R 0.408602 0.763158
279 A4P 0.407407 0.659091
280 UP5 0.40566 0.734177
281 F2R 0.405405 0.674419
282 6MZ 0.404762 0.808219
283 IOT 0.40367 0.666667
284 6CR 0.402597 0.805556
285 TYM 0.401869 0.74359
286 WSA 0.401869 0.686047
287 N37 0.401869 0.780822
288 AF3 ADP 3PG 0.401869 0.707317
289 4TA 0.401786 0.702381
290 YLA 0.4 0.674419
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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