Receptor
PDB id Resolution Class Description Source Keywords
3V8Q 2.37 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 H223E MUTANT FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH 5'-AMINO-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
5N5 A:301;
Valid;
none;
submit data
266.257 C10 H14 N6 O3 c1nc(...
CIT A:303;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
GOL A:302;
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: 5N5; Similar ligands found: 278
No: Ligand ECFP6 Tc MDL keys Tc
1 5N5 1 1
2 RAB 0.811321 0.967742
3 ADN 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 AMP 0.661538 0.816901
14 LMS 0.661538 0.716049
15 A 0.661538 0.816901
16 ZAS 0.661538 0.867647
17 SRA 0.651515 0.773333
18 6RE 0.651515 0.857143
19 5AD 0.649123 0.854839
20 S4M 0.647059 0.789474
21 AOC 0.641791 0.878788
22 A2D 0.632353 0.819444
23 A3N 0.632353 0.953125
24 J7C 0.632353 0.869565
25 ABM 0.632353 0.794521
26 GJV 0.623188 0.84507
27 AP2 0.614286 0.786667
28 A12 0.614286 0.786667
29 MAO 0.614286 0.75641
30 BA3 0.614286 0.819444
31 M33 0.611111 0.808219
32 7D7 0.610169 0.846154
33 Y3J 0.606557 0.828125
34 B4P 0.605634 0.819444
35 ADP 0.605634 0.819444
36 AP5 0.605634 0.819444
37 5AS 0.605634 0.714286
38 A7D 0.597222 0.880597
39 SON 0.597222 0.763158
40 AT4 0.597222 0.786667
41 AN2 0.597222 0.808219
42 AU1 0.589041 0.797297
43 CA0 0.589041 0.797297
44 ADX 0.589041 0.7375
45 MHZ 0.589041 0.779221
46 ADP PO3 0.586667 0.816901
47 A5D 0.586667 0.865672
48 SFG 0.581081 0.850746
49 50T 0.581081 0.808219
50 ATP 0.581081 0.819444
51 5X8 0.581081 0.865672
52 ACP 0.581081 0.797297
53 HEJ 0.581081 0.819444
54 G5A 0.578947 0.714286
55 3AM 0.573529 0.802817
56 5FA 0.573333 0.819444
57 AR6 0.573333 0.819444
58 APC 0.573333 0.786667
59 PRX 0.573333 0.773333
60 AQP 0.573333 0.819444
61 APR 0.573333 0.819444
62 A3G 0.571429 0.938462
63 AGS 0.565789 0.776316
64 SA8 0.565789 0.819444
65 AD9 0.565789 0.797297
66 SAP 0.565789 0.776316
67 ADV 0.565789 0.786667
68 RBY 0.565789 0.786667
69 AAT 0.564103 0.84507
70 SAI 0.558442 0.828571
71 SAH 0.558442 0.84058
72 A5A 0.556962 0.698795
73 GAP 0.551282 0.821918
74 ANP 0.551282 0.797297
75 T99 0.551282 0.786667
76 SAM 0.551282 0.773333
77 TAT 0.551282 0.786667
78 ACQ 0.551282 0.797297
79 NEC 0.549296 0.90625
80 3AD 0.546875 0.920635
81 EEM 0.544304 0.773333
82 5AL 0.544304 0.783784
83 ADP ALF 0.5375 0.753247
84 ALF ADP 0.5375 0.753247
85 ATF 0.5375 0.786667
86 53H 0.536585 0.674419
87 8X1 0.536585 0.689655
88 2AM 0.536232 0.816901
89 CC5 0.532258 0.904762
90 6YZ 0.530864 0.797297
91 S7M 0.530864 0.773333
92 SRP 0.530864 0.786667
93 SSA 0.530864 0.714286
94 VO4 ADP 0.530864 0.783784
95 SMM 0.530864 0.74359
96 ADP VO4 0.530864 0.783784
97 A3P 0.527027 0.791667
98 VMS 0.52439 0.682353
99 52H 0.52439 0.674419
100 54H 0.52439 0.682353
101 7D5 0.521739 0.756757
102 QQY 0.521127 0.743243
103 DAL AMP 0.518072 0.783784
104 A22 0.518072 0.808219
105 5CA 0.518072 0.714286
106 TSB 0.518072 0.710843
107 MAP 0.518072 0.776316
108 OVE 0.513889 0.783784
109 A3S 0.513158 0.923077
110 5SV 0.511905 0.734177
111 25A 0.511905 0.794521
112 S8M 0.511905 0.805556
113 GEK 0.511905 0.805556
114 9ZD 0.511905 0.74359
115 9ZA 0.511905 0.74359
116 8QN 0.511905 0.783784
117 OOB 0.511905 0.783784
118 A6D 0.511628 0.763158
119 QQX 0.507042 0.733333
120 A1R 0.505882 0.813333
121 ADQ 0.505882 0.821918
122 NSS 0.505882 0.694118
123 A3R 0.505882 0.813333
124 4AD 0.505882 0.776316
125 DSZ 0.505882 0.694118
126 PAJ 0.505882 0.769231
127 0UM 0.505882 0.833333
128 AMO 0.505882 0.786667
129 LSS 0.505882 0.659091
130 LAD 0.505747 0.769231
131 KAA 0.505747 0.689655
132 PTJ 0.5 0.734177
133 ACK 0.5 0.785714
134 JB6 0.5 0.74359
135 SP1 0.5 0.746667
136 TXA 0.5 0.786667
137 NVA LMS 0.5 0.651685
138 62X 0.5 0.766234
139 RP1 0.5 0.746667
140 A3T 0.5 0.9375
141 3D1 0.5 0.878788
142 AHX 0.5 0.779221
143 3L1 0.5 0.878788
144 DLL 0.5 0.783784
145 00A 0.5 0.74359
146 9X8 0.494253 0.776316
147 OAD 0.494253 0.797297
148 K15 0.494253 0.786667
149 3UK 0.494253 0.773333
150 LEU LMS 0.494253 0.651685
151 ADP BMA 0.494253 0.821918
152 2FA 0.492537 0.895522
153 26A 0.492537 0.865672
154 PR8 0.488636 0.759494
155 P5A 0.488636 0.681818
156 WAQ 0.488636 0.74359
157 B5V 0.488636 0.763158
158 A A 0.488636 0.794521
159 GSU 0.488636 0.674419
160 PAP 0.4875 0.805556
161 A2P 0.486842 0.777778
162 2BA 0.486842 0.788732
163 CMP 0.486842 0.8
164 5F1 0.485294 0.80597
165 YAP 0.483516 0.753247
166 ATP A A A 0.483516 0.805556
167 3OD 0.483146 0.797297
168 ME8 0.483146 0.707317
169 SXZ 0.483146 0.773333
170 BIS 0.483146 0.766234
171 1ZZ 0.483146 0.707317
172 NB8 0.483146 0.75641
173 9K8 0.483146 0.651685
174 FYA 0.483146 0.783784
175 7MD 0.478723 0.772152
176 XAH 0.478261 0.75
177 YSA 0.478261 0.674419
178 25L 0.477778 0.808219
179 MYR AMP 0.477778 0.707317
180 KB1 0.477778 0.808219
181 MTP 0.477612 0.826087
182 V3L 0.47561 0.794521
183 7D3 0.473684 0.76
184 9SN 0.472527 0.734177
185 1DA 0.470588 0.967742
186 6MD 0.470588 0.921875
187 PPS 0.46988 0.716049
188 NOC 0.469697 0.873016
189 B5Y 0.467391 0.753247
190 B5M 0.467391 0.753247
191 FA5 0.467391 0.763158
192 8PZ 0.467391 0.694118
193 D3Y 0.465116 0.895522
194 AR6 AR6 0.463158 0.794521
195 2VA 0.4625 0.909091
196 GTA 0.458333 0.728395
197 TYR AMP 0.457447 0.753247
198 4UV 0.457447 0.753247
199 AMP DBH 0.457447 0.797297
200 2A5 0.45679 0.773333
201 G3A 0.452632 0.75641
202 7C5 0.452632 0.794521
203 ATR 0.451219 0.791667
204 NVA 2AD 0.451219 0.857143
205 7D4 0.45 0.76
206 ARJ 0.449275 0.828125
207 5NB 0.449275 0.910448
208 ARG AMP 0.447917 0.740741
209 G5P 0.447917 0.75641
210 AFH 0.447917 0.769231
211 GA7 0.447917 0.810811
212 4UU 0.447917 0.753247
213 VRT 0.445783 0.869565
214 SO8 0.445783 0.895522
215 6V0 0.444444 0.779221
216 TAD 0.443299 0.746835
217 DQV 0.443299 0.808219
218 4YB 0.443299 0.659091
219 KH3 0.443299 0.8
220 3NZ 0.43956 0.857143
221 LAQ 0.438776 0.707317
222 AHZ 0.438776 0.707317
223 A2R 0.436782 0.808219
224 YLC 0.435644 0.75
225 7MC 0.435644 0.753086
226 YLP 0.434343 0.731707
227 LPA AMP 0.434343 0.707317
228 48N 0.434343 0.75641
229 101 0.434211 0.756757
230 NAI 0.43 0.766234
231 UP5 0.43 0.776316
232 NAX 0.43 0.7375
233 DND 0.43 0.786667
234 4UW 0.43 0.725
235 NXX 0.43 0.786667
236 TXD 0.43 0.789474
237 A A A 0.428571 0.783784
238 PO4 PO4 A A A A PO4 0.428571 0.777778
239 AFX 0.428571 0.742857
240 IOT 0.427184 0.722892
241 OMR 0.425743 0.719512
242 TXE 0.425743 0.789474
243 649 0.425743 0.644444
244 AF3 ADP 3PG 0.425743 0.725
245 TYM 0.425743 0.763158
246 WSA 0.425743 0.682353
247 YLB 0.421569 0.731707
248 F0P 0.421569 0.819444
249 4TC 0.421569 0.75641
250 8Q2 0.421569 0.670455
251 UPA 0.421569 0.789474
252 AP0 0.421569 0.75641
253 CNA 0.419048 0.786667
254 A4P 0.417476 0.73494
255 6CR 0.416667 0.882353
256 5J9 0.414894 0.773333
257 AV2 0.413793 0.746667
258 V1N 0.412371 0.794521
259 NAD 0.411215 0.783784
260 D5M 0.410256 0.733333
261 DA 0.410256 0.733333
262 ADJ 0.409524 0.740741
263 YLA 0.409524 0.731707
264 T5A 0.409524 0.710843
265 139 0.409524 0.759494
266 DZD 0.407407 0.769231
267 J1D 0.407407 0.642105
268 IVH 0.407407 0.810811
269 3AT 0.406977 0.794521
270 BS5 0.40566 0.693182
271 AYB 0.40566 0.722892
272 IMO 0.405063 0.753425
273 AS 0.405063 0.696203
274 0XU 0.404762 0.823529
275 AD3 0.402778 0.967742
276 F2R 0.401869 0.753086
277 EO7 0.4 0.682353
278 GGZ 0.4 0.691358
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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