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: 266
No: Ligand ECFP6 Tc MDL keys Tc
1 AOC 1 1
2 AMP 0.666667 0.84507
3 A 0.666667 0.84507
4 ADN 0.661538 0.907692
5 RAB 0.661538 0.907692
6 XYA 0.661538 0.907692
7 SRA 0.657534 0.8
8 SON 0.649351 0.789474
9 AMP MG 0.648649 0.821918
10 5N5 0.641791 0.878788
11 A3N 0.64 0.924242
12 A2D 0.64 0.821918
13 ABM 0.64 0.821918
14 5CD 0.632353 0.892308
15 A4D 0.632353 0.878788
16 A12 0.623377 0.789474
17 BA3 0.623377 0.821918
18 AP2 0.623377 0.789474
19 AU1 0.620253 0.8
20 AP5 0.615385 0.821918
21 5AS 0.615385 0.697674
22 ADP 0.615385 0.821918
23 B4P 0.615385 0.821918
24 AN2 0.607595 0.810811
25 EP4 0.605634 0.855072
26 ADX 0.6 0.740741
27 M33 0.6 0.810811
28 CA0 0.6 0.8
29 ADP MG 0.6 0.810811
30 DTA 0.597222 0.84058
31 M2T 0.597222 0.830986
32 3DH 0.594595 0.880597
33 ADP BEF 0.592593 0.789474
34 ATP 0.592593 0.821918
35 50T 0.592593 0.810811
36 ACP 0.592593 0.8
37 BEF ADP 0.592593 0.789474
38 MTA 0.589041 0.880597
39 PRX 0.585366 0.8
40 APC 0.585366 0.789474
41 AQP 0.585366 0.821918
42 5FA 0.585366 0.821918
43 APR 0.585366 0.821918
44 AR6 0.585366 0.821918
45 RBY 0.578313 0.789474
46 ADV 0.578313 0.789474
47 AD9 0.578313 0.8
48 ADP PO3 0.578313 0.84507
49 AGS 0.578313 0.779221
50 SAP 0.578313 0.779221
51 G5A 0.571429 0.697674
52 ATP MG 0.571429 0.810811
53 ADP ALF 0.569767 0.779221
54 ALF ADP 0.569767 0.779221
55 GAP 0.564706 0.8
56 TAT 0.564706 0.789474
57 ACQ 0.564706 0.8
58 ANP 0.564706 0.8
59 OOB 0.561798 0.810811
60 5AD 0.558824 0.828125
61 ZAS 0.558442 0.816901
62 5AL 0.55814 0.810811
63 A5A 0.551724 0.722892
64 ATF 0.551724 0.789474
65 6RE 0.551282 0.783784
66 ADP VO4 0.545455 0.810811
67 ANP MG 0.545455 0.779221
68 SSA 0.545455 0.697674
69 SRP 0.545455 0.789474
70 VO4 ADP 0.545455 0.810811
71 5SV 0.544444 0.759494
72 DSH 0.544304 0.819444
73 MAO 0.54321 0.782051
74 52H 0.539326 0.697674
75 54H 0.539326 0.705882
76 VMS 0.539326 0.705882
77 ADQ 0.538462 0.8
78 PAJ 0.538462 0.75
79 J7C 0.5375 0.794521
80 DAL AMP 0.533333 0.810811
81 TSB 0.533333 0.714286
82 5CA 0.533333 0.697674
83 53H 0.533333 0.697674
84 MAP 0.533333 0.779221
85 A22 0.533333 0.810811
86 DLL 0.532609 0.810811
87 00A 0.532609 0.769231
88 1ZZ 0.531915 0.731707
89 S4M 0.530864 0.746835
90 GJV 0.530864 0.773333
91 7D7 0.528571 0.820895
92 8QN 0.527473 0.810811
93 25A 0.527473 0.821918
94 LEU LMS 0.526882 0.681818
95 ADP BMA 0.526882 0.8
96 3UK 0.526882 0.8
97 MYR AMP 0.526316 0.731707
98 AMO 0.521739 0.789474
99 A1R 0.521739 0.769231
100 DSZ 0.521739 0.697674
101 LSS 0.521739 0.681818
102 4AD 0.521739 0.779221
103 NSS 0.521739 0.697674
104 A A 0.521277 0.821918
105 WAQ 0.521277 0.769231
106 P5A 0.521277 0.666667
107 GSU 0.521277 0.697674
108 AMP DBH 0.520408 0.8
109 5X8 0.517647 0.867647
110 SFG 0.517647 0.826087
111 NVA LMS 0.516129 0.681818
112 AHX 0.516129 0.759494
113 3OD 0.515789 0.8
114 FYA 0.515789 0.810811
115 PTJ 0.515789 0.759494
116 7C5 0.515152 0.821918
117 A7D 0.511905 0.882353
118 OAD 0.510638 0.8
119 Y3J 0.506849 0.80303
120 3AM 0.506329 0.805556
121 MHZ 0.505882 0.7375
122 A5D 0.505747 0.84058
123 KAA 0.505263 0.674157
124 PR8 0.505263 0.740741
125 LAD 0.505263 0.75
126 9SN 0.505155 0.759494
127 JB6 0.5 0.769231
128 FA5 0.5 0.789474
129 NB8 0.5 0.759494
130 YAP 0.5 0.779221
131 ATP A A A 0.5 0.833333
132 TXA 0.5 0.789474
133 BIS 0.5 0.769231
134 ME8 0.5 0.753086
135 YLA 0.495327 0.756098
136 YSA 0.494949 0.697674
137 TYR AMP 0.494949 0.789474
138 25L 0.494845 0.810811
139 4YB 0.490196 0.681818
140 AAT 0.488889 0.797297
141 SA8 0.488636 0.797297
142 A3P 0.488095 0.819444
143 SAH 0.483146 0.842857
144 SAI 0.483146 0.830986
145 7D5 0.481013 0.76
146 7MD 0.480392 0.731707
147 AFH 0.480392 0.75
148 XAH 0.48 0.731707
149 SMM 0.478261 0.769231
150 SAM 0.477778 0.776316
151 NXX 0.47619 0.789474
152 NAI 0.47619 0.792208
153 DND 0.47619 0.789474
154 4UV 0.475248 0.802632
155 2AM 0.475 0.794521
156 EEM 0.472527 0.776316
157 OMR 0.471698 0.722892
158 649 0.471698 0.666667
159 AHZ 0.471154 0.731707
160 LAQ 0.471154 0.731707
161 G3A 0.470588 0.759494
162 A2P 0.470588 0.805556
163 A3G 0.46988 0.855072
164 NEC 0.46988 0.797101
165 LPA AMP 0.466667 0.731707
166 4UU 0.466019 0.802632
167 AR6 AR6 0.466019 0.821918
168 G5P 0.466019 0.759494
169 CC5 0.465753 0.90625
170 S7M 0.462366 0.776316
171 GTA 0.461538 0.731707
172 TAD 0.461538 0.75
173 3AD 0.460526 0.892308
174 0UM 0.458333 0.763158
175 TYM 0.457944 0.789474
176 AF3 ADP 3PG 0.457944 0.75
177 TXE 0.457944 0.792208
178 WSA 0.457944 0.705882
179 OVE 0.457831 0.763158
180 ARG AMP 0.457143 0.722892
181 PAP 0.455556 0.808219
182 YLB 0.453704 0.714286
183 7MC 0.453704 0.714286
184 48N 0.45283 0.759494
185 YLP 0.45283 0.714286
186 A6D 0.44898 0.74359
187 K15 0.44898 0.766234
188 6V0 0.448598 0.782051
189 TXD 0.448598 0.815789
190 UP5 0.448598 0.802632
191 NAX 0.448598 0.7625
192 4UW 0.448598 0.772152
193 GEK 0.447917 0.808219
194 S8M 0.447917 0.808219
195 QQY 0.445783 0.723684
196 V3L 0.445652 0.821918
197 2A5 0.444444 0.753247
198 ALF ADP 3PG 0.444444 0.75
199 LA8 ALF 3PG 0.444444 0.75
200 SLU 0.443478 0.689655
201 A3S 0.443182 0.867647
202 NAD 0.442478 0.810811
203 7D3 0.44186 0.74026
204 T5A 0.441441 0.73494
205 PPS 0.44086 0.719512
206 YLC 0.440367 0.753086
207 AP0 0.440367 0.782051
208 4TC 0.440367 0.782051
209 UPA 0.440367 0.792208
210 ATR 0.43956 0.794521
211 62X 0.438776 0.746835
212 DZD 0.438596 0.772152
213 7D4 0.438202 0.74026
214 CNA 0.4375 0.789474
215 A4P 0.436364 0.717647
216 KB1 0.435644 0.786667
217 A3D 0.434783 0.8
218 QQX 0.433735 0.714286
219 NAD IBO 0.433628 0.779221
220 A3T 0.433333 0.880597
221 IOT 0.432432 0.705882
222 IMO 0.430233 0.780822
223 G A A A 0.429825 0.759494
224 COD 0.429825 0.689655
225 4TA 0.429825 0.743902
226 ACK 0.428571 0.763889
227 RP1 0.428571 0.75
228 SP1 0.428571 0.75
229 ADJ 0.428571 0.765432
230 139 0.428571 0.7625
231 A2R 0.427083 0.810811
232 BT5 0.426087 0.705882
233 SXZ 0.425743 0.776316
234 AYB 0.424779 0.705882
235 M24 0.423729 0.740741
236 3L1 0.423077 0.826087
237 MTP 0.423077 0.777778
238 3D1 0.423077 0.826087
239 2BA 0.420455 0.791667
240 CMP 0.420455 0.802817
241 NAE 0.420168 0.779221
242 PO4 PO4 A A A A PO4 0.42 0.805556
243 A A A 0.42 0.810811
244 NAJ PZO 0.418803 0.782051
245 26A 0.417722 0.84058
246 2FA 0.417722 0.842857
247 2VA 0.417582 0.855072
248 BTX 0.417391 0.714286
249 NAQ 0.416667 0.759494
250 U A G G 0.413793 0.769231
251 AMP NAD 0.413223 0.789474
252 ZID 0.413223 0.8
253 5F1 0.4125 0.782609
254 YLY 0.411765 0.705882
255 D3Y 0.408163 0.842857
256 KH3 0.407407 0.75641
257 ITT 0.406593 0.77027
258 PGS 0.406593 0.725
259 NA7 0.405941 0.789474
260 NAJ PYZ 0.404959 0.740741
261 NDE 0.404762 0.789474
262 SO8 0.404255 0.842857
263 3NZ 0.401961 0.833333
264 3AT 0.4 0.797297
265 6MD 0.4 0.865672
266 1DA 0.4 0.907692
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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