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: 266
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 A4D 0.767857 0.967742
6 5CD 0.767857 0.920635
7 EP4 0.728814 0.880597
8 M2T 0.716667 0.828571
9 DTA 0.716667 0.865672
10 MTA 0.704918 0.878788
11 3DH 0.68254 0.878788
12 DSH 0.666667 0.869565
13 A 0.661538 0.816901
14 ZAS 0.661538 0.867647
15 AMP 0.661538 0.816901
16 6RE 0.651515 0.857143
17 SRA 0.651515 0.773333
18 5AD 0.649123 0.854839
19 S4M 0.647059 0.789474
20 AOC 0.641791 0.878788
21 AMP MG 0.641791 0.794521
22 A2D 0.632353 0.819444
23 ABM 0.632353 0.794521
24 J7C 0.632353 0.869565
25 A3N 0.632353 0.953125
26 GJV 0.623188 0.84507
27 AP2 0.614286 0.786667
28 MAO 0.614286 0.75641
29 BA3 0.614286 0.819444
30 A12 0.614286 0.786667
31 M33 0.611111 0.808219
32 7D7 0.610169 0.846154
33 Y3J 0.606557 0.828125
34 5AS 0.605634 0.714286
35 AP5 0.605634 0.819444
36 ADP 0.605634 0.819444
37 B4P 0.605634 0.819444
38 AN2 0.597222 0.808219
39 SON 0.597222 0.763158
40 A7D 0.597222 0.880597
41 ADP MG 0.589041 0.783784
42 CA0 0.589041 0.797297
43 AU1 0.589041 0.797297
44 MHZ 0.589041 0.779221
45 ADX 0.589041 0.7375
46 ADP PO3 0.586667 0.816901
47 A5D 0.586667 0.865672
48 ATP 0.581081 0.819444
49 5X8 0.581081 0.865672
50 ADP BEF 0.581081 0.763158
51 SFG 0.581081 0.850746
52 ACP 0.581081 0.797297
53 50T 0.581081 0.808219
54 BEF ADP 0.581081 0.763158
55 G5A 0.578947 0.714286
56 ATP MG 0.578947 0.783784
57 3AM 0.573529 0.802817
58 APC 0.573333 0.786667
59 AR6 0.573333 0.819444
60 PRX 0.573333 0.773333
61 APR 0.573333 0.819444
62 5FA 0.573333 0.819444
63 AQP 0.573333 0.819444
64 A3G 0.571429 0.938462
65 AD9 0.565789 0.797297
66 AGS 0.565789 0.776316
67 ADV 0.565789 0.786667
68 SAP 0.565789 0.776316
69 RBY 0.565789 0.786667
70 SA8 0.565789 0.819444
71 AAT 0.564103 0.84507
72 SAI 0.558442 0.828571
73 SAH 0.558442 0.84058
74 A5A 0.556962 0.698795
75 ACQ 0.551282 0.797297
76 SAM 0.551282 0.773333
77 TAT 0.551282 0.786667
78 GAP 0.551282 0.821918
79 ANP 0.551282 0.797297
80 NEC 0.549296 0.90625
81 3AD 0.546875 0.920635
82 EEM 0.544304 0.773333
83 5AL 0.544304 0.783784
84 ALF ADP 0.5375 0.753247
85 ADP ALF 0.5375 0.753247
86 ATF 0.5375 0.786667
87 53H 0.536585 0.674419
88 2AM 0.536232 0.816901
89 CC5 0.532258 0.904762
90 VO4 ADP 0.530864 0.783784
91 ADP VO4 0.530864 0.783784
92 SMM 0.530864 0.74359
93 S7M 0.530864 0.773333
94 SSA 0.530864 0.714286
95 SRP 0.530864 0.786667
96 ANP MG 0.530864 0.753247
97 A3P 0.527027 0.791667
98 54H 0.52439 0.682353
99 52H 0.52439 0.674419
100 VMS 0.52439 0.682353
101 7D5 0.521739 0.756757
102 QQY 0.521127 0.743243
103 5CA 0.518072 0.714286
104 A22 0.518072 0.808219
105 DAL AMP 0.518072 0.783784
106 MAP 0.518072 0.776316
107 TSB 0.518072 0.710843
108 OVE 0.513889 0.783784
109 A3S 0.513158 0.923077
110 S8M 0.511905 0.805556
111 8QN 0.511905 0.783784
112 GEK 0.511905 0.805556
113 5SV 0.511905 0.734177
114 OOB 0.511905 0.783784
115 25A 0.511905 0.794521
116 A6D 0.511628 0.763158
117 QQX 0.507042 0.733333
118 ADQ 0.505882 0.821918
119 4AD 0.505882 0.776316
120 0UM 0.505882 0.833333
121 DSZ 0.505882 0.694118
122 AMO 0.505882 0.786667
123 PAJ 0.505882 0.769231
124 A1R 0.505882 0.813333
125 LSS 0.505882 0.659091
126 NSS 0.505882 0.694118
127 KAA 0.505747 0.689655
128 LAD 0.505747 0.769231
129 3L1 0.5 0.878788
130 TXA 0.5 0.786667
131 3D1 0.5 0.878788
132 AHX 0.5 0.779221
133 PTJ 0.5 0.734177
134 JB6 0.5 0.74359
135 A3T 0.5 0.9375
136 RP1 0.5 0.746667
137 00A 0.5 0.74359
138 DLL 0.5 0.783784
139 ACK 0.5 0.785714
140 62X 0.5 0.766234
141 SP1 0.5 0.746667
142 NVA LMS 0.5 0.659091
143 OAD 0.494253 0.797297
144 K15 0.494253 0.786667
145 LEU LMS 0.494253 0.659091
146 ADP BMA 0.494253 0.821918
147 3UK 0.494253 0.773333
148 2FA 0.492537 0.895522
149 26A 0.492537 0.865672
150 A A 0.488636 0.794521
151 PR8 0.488636 0.759494
152 WAQ 0.488636 0.74359
153 GSU 0.488636 0.674419
154 P5A 0.488636 0.681818
155 PAP 0.4875 0.805556
156 CMP 0.486842 0.8
157 A2P 0.486842 0.777778
158 2BA 0.486842 0.788732
159 5F1 0.485294 0.80597
160 ATP A A A 0.483516 0.805556
161 YAP 0.483516 0.753247
162 BIS 0.483146 0.766234
163 FYA 0.483146 0.783784
164 SXZ 0.483146 0.773333
165 NB8 0.483146 0.75641
166 1ZZ 0.483146 0.707317
167 ME8 0.483146 0.707317
168 3OD 0.483146 0.797297
169 7MD 0.478723 0.772152
170 YSA 0.478261 0.674419
171 XAH 0.478261 0.75
172 KB1 0.477778 0.808219
173 MYR AMP 0.477778 0.707317
174 25L 0.477778 0.808219
175 MTP 0.477612 0.826087
176 V3L 0.47561 0.794521
177 7D3 0.473684 0.76
178 9SN 0.472527 0.734177
179 1DA 0.470588 0.967742
180 6MD 0.470588 0.921875
181 PPS 0.46988 0.716049
182 NOC 0.469697 0.873016
183 FA5 0.467391 0.763158
184 D3Y 0.465116 0.895522
185 AR6 AR6 0.463158 0.794521
186 2VA 0.4625 0.909091
187 TYR AMP 0.462366 0.763158
188 GTA 0.458333 0.728395
189 4UV 0.457447 0.753247
190 AMP DBH 0.457447 0.797297
191 2A5 0.45679 0.773333
192 G3A 0.452632 0.75641
193 7C5 0.452632 0.794521
194 NVA 2AD 0.451219 0.84058
195 ATR 0.451219 0.791667
196 7D4 0.45 0.76
197 ARJ 0.449275 0.828125
198 5NB 0.449275 0.910448
199 4UU 0.447917 0.753247
200 G5P 0.447917 0.75641
201 AFH 0.447917 0.769231
202 SO8 0.445783 0.895522
203 VRT 0.445783 0.869565
204 6V0 0.444444 0.779221
205 KH3 0.443299 0.8
206 4YB 0.443299 0.659091
207 TAD 0.443299 0.746835
208 3NZ 0.43956 0.857143
209 AHZ 0.438776 0.707317
210 LAQ 0.438776 0.707317
211 ARG AMP 0.438776 0.740741
212 A2R 0.436782 0.808219
213 YLC 0.435644 0.75
214 7MC 0.435644 0.753086
215 48N 0.434343 0.75641
216 LPA AMP 0.434343 0.707317
217 YLP 0.434343 0.731707
218 101 0.434211 0.756757
219 UP5 0.43 0.776316
220 NXX 0.43 0.786667
221 NAX 0.43 0.7375
222 NAI 0.43 0.766234
223 DND 0.43 0.786667
224 TXD 0.43 0.789474
225 4UW 0.43 0.725
226 AFX 0.428571 0.742857
227 A A A 0.428571 0.783784
228 PO4 PO4 A A A A PO4 0.428571 0.777778
229 IOT 0.427184 0.722892
230 WSA 0.425743 0.682353
231 649 0.425743 0.644444
232 OMR 0.425743 0.719512
233 TXE 0.425743 0.789474
234 ALF ADP 3PG 0.425743 0.725
235 AF3 ADP 3PG 0.425743 0.725
236 TYM 0.425743 0.763158
237 LA8 ALF 3PG 0.425743 0.725
238 4TC 0.421569 0.75641
239 YLB 0.421569 0.731707
240 UPA 0.421569 0.789474
241 AP0 0.421569 0.75641
242 CNA 0.419048 0.786667
243 A4P 0.417476 0.73494
244 6CR 0.416667 0.882353
245 NAD IBO 0.415094 0.753247
246 5J9 0.414894 0.773333
247 AV2 0.413793 0.746667
248 V1N 0.412371 0.794521
249 NAD 0.411215 0.783784
250 D5M 0.410256 0.733333
251 DA 0.410256 0.733333
252 139 0.409524 0.759494
253 ADJ 0.409524 0.740741
254 YLA 0.409524 0.731707
255 T5A 0.409524 0.710843
256 J1D 0.407407 0.642105
257 IVH 0.407407 0.810811
258 DZD 0.407407 0.769231
259 3AT 0.406977 0.794521
260 AYB 0.40566 0.722892
261 BS5 0.40566 0.693182
262 IMO 0.405063 0.753425
263 AS 0.405063 0.696203
264 0XU 0.404762 0.823529
265 AD3 0.402778 0.967742
266 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: 16
This union binding pocket(no: 1) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SJN DUP 0.04055 0.40415 1.17647
2 3B6C SDN 0.03486 0.4278 2.5641
3 1M2Z BOG 0.01657 0.46108 3.89105
4 3HCH RSM 0.03204 0.43257 4.10959
5 2D3Y DU 0.03479 0.44206 4.41176
6 1DJ9 KAM 0.0401 0.40726 4.77941
7 4OAS 2SW 0.02718 0.41911 5.20833
8 3KO0 TFP 0.02073 0.44449 5.94059
9 5FPE 3TR 0.01038 0.4641 6.25
10 3SAO DBH 0.03256 0.43022 6.875
11 5KAU RHQ 0.02012 0.4164 7.87879
12 2DUR MAN MAN 0.03876 0.41998 8.3004
13 3V2U ATP 0.03218 0.40114 10.2941
14 4LWU 20U 0.009015 0.44397 10.5882
15 3ZC7 ATP 0.03378 0.41418 11.1111
16 1LNX URI 0.04192 0.42585 37.037
Pocket No.: 2; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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