Receptor
PDB id Resolution Class Description Source Keywords
2Q5F 1.9 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES LISTERIA MONOCYTOGENES EGD-E MUTANT TRANSFERASE
Ref.: NAD KINASES USE SUBSTRATE-ASSISTED CATALYSIS FOR SP RECOGNITION OF NAD. J.BIOL.CHEM. V. 282 33925 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DTA A:273;
Valid;
none;
Ki = 0.02 mM
564.598 C20 H24 N10 O6 S2 c1nc(...
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: DTA; Similar ligands found: 253
No: Ligand ECFP6 Tc MDL keys Tc
1 DTA 1 1
2 3DH 0.790323 0.867647
3 MTA 0.786885 0.867647
4 A5D 0.746479 1
5 DSH 0.742424 0.833333
6 ADN 0.741379 0.865672
7 XYA 0.741379 0.865672
8 RAB 0.741379 0.865672
9 5CD 0.733333 0.878788
10 5N5 0.716667 0.865672
11 A4D 0.704918 0.893939
12 5X8 0.694444 0.855072
13 A7D 0.690141 0.869565
14 EP4 0.671875 0.816901
15 SAH 0.666667 0.857143
16 M2T 0.661538 0.819444
17 A6D 0.646341 0.876712
18 A 0.637681 0.808219
19 AMP 0.637681 0.808219
20 SRA 0.628571 0.813333
21 ZAS 0.614286 0.830986
22 J7C 0.611111 0.783784
23 AAT 0.607595 0.810811
24 6RE 0.605634 0.773333
25 AMP MG 0.597222 0.786667
26 AOC 0.597222 0.84058
27 5AD 0.596774 0.815385
28 S8M 0.590361 0.847222
29 A3N 0.589041 0.828571
30 A2D 0.589041 0.810811
31 ABM 0.589041 0.786667
32 S4M 0.581081 0.759494
33 GJV 0.581081 0.763158
34 SON 0.578947 0.779221
35 SXZ 0.574713 0.789474
36 MAO 0.573333 0.75
37 BA3 0.573333 0.810811
38 AP2 0.573333 0.779221
39 A12 0.573333 0.779221
40 CA0 0.571429 0.766234
41 ADX 0.571429 0.753086
42 AP5 0.565789 0.810811
43 B4P 0.565789 0.810811
44 5AS 0.565789 0.709302
45 ADP 0.565789 0.786667
46 50T 0.564103 0.776316
47 SFG 0.564103 0.84058
48 7D7 0.5625 0.808824
49 Y3J 0.560606 0.791045
50 AN2 0.558442 0.776316
51 AU1 0.551282 0.766234
52 MHZ 0.551282 0.75
53 M33 0.551282 0.776316
54 ADP MG 0.551282 0.776316
55 SA8 0.55 0.786667
56 EEM 0.548781 0.766234
57 ACP 0.544304 0.766234
58 ADP BEF 0.544304 0.75641
59 ATP 0.544304 0.786667
60 BEF ADP 0.544304 0.75641
61 SAI 0.54321 0.819444
62 G5A 0.54321 0.709302
63 5FA 0.5375 0.786667
64 PRX 0.5375 0.766234
65 APC 0.5375 0.779221
66 AR6 0.5375 0.786667
67 AQP 0.5375 0.786667
68 APR 0.5375 0.786667
69 SAM 0.536585 0.789474
70 GAP 0.536585 0.766234
71 SRP 0.535714 0.75641
72 SMM 0.535714 0.759494
73 3AM 0.534247 0.77027
74 NEC 0.533333 0.785714
75 A3G 0.533333 0.816901
76 SAP 0.530864 0.792208
77 ADV 0.530864 0.779221
78 RBY 0.530864 0.779221
79 AGS 0.530864 0.792208
80 ADP PO3 0.530864 0.808219
81 AD9 0.530864 0.766234
82 5AL 0.53012 0.776316
83 ATP MG 0.52439 0.776316
84 A5A 0.52381 0.73494
85 ANP 0.518072 0.766234
86 TAT 0.518072 0.802632
87 ACQ 0.518072 0.766234
88 ADP VO4 0.517647 0.776316
89 VO4 ADP 0.517647 0.776316
90 SSA 0.517647 0.709302
91 S7M 0.517647 0.789474
92 8QN 0.517241 0.776316
93 A3P 0.512821 0.783784
94 54H 0.511628 0.717647
95 VMS 0.511628 0.717647
96 52H 0.511628 0.709302
97 3AD 0.507246 0.850746
98 7D5 0.506849 0.75
99 ATF 0.505882 0.75641
100 ALF ADP 0.505882 0.746835
101 ADP ALF 0.505882 0.746835
102 DAL AMP 0.505747 0.776316
103 53H 0.505747 0.709302
104 TSB 0.505747 0.72619
105 5CA 0.505747 0.709302
106 00A 0.505618 0.759494
107 AHX 0.505618 0.728395
108 25A 0.5 0.810811
109 2AM 0.5 0.76
110 A3S 0.5 0.828571
111 3UK 0.5 0.789474
112 ANP MG 0.5 0.746835
113 OOB 0.5 0.8
114 GEK 0.5 0.821918
115 4AD 0.494382 0.746835
116 DSZ 0.494382 0.709302
117 LSS 0.494382 0.693182
118 NSS 0.494382 0.709302
119 0UM 0.494382 0.776316
120 PAJ 0.494382 0.719512
121 AMO 0.494382 0.75641
122 CC5 0.492537 0.863636
123 ME8 0.48913 0.722892
124 NVA LMS 0.488889 0.693182
125 62X 0.488889 0.7375
126 DLL 0.488889 0.8
127 MAP 0.488636 0.746835
128 A22 0.488636 0.8
129 A3T 0.487805 0.84058
130 LEU LMS 0.483516 0.693182
131 K15 0.483516 0.75641
132 OAD 0.483516 0.766234
133 5SV 0.483146 0.75
134 OVE 0.480519 0.776316
135 PR8 0.478261 0.731707
136 WAQ 0.478261 0.759494
137 GSU 0.478261 0.709302
138 KAA 0.478261 0.704545
139 LAD 0.478261 0.740741
140 P5A 0.478261 0.696629
141 ADQ 0.477778 0.789474
142 A1R 0.477778 0.759494
143 A2P 0.475 0.77027
144 QQX 0.473684 0.75
145 NB8 0.473118 0.728395
146 PTJ 0.473118 0.728395
147 1ZZ 0.473118 0.722892
148 TXA 0.473118 0.75641
149 3OD 0.473118 0.766234
150 2VA 0.46988 0.816901
151 TYR AMP 0.46875 0.779221
152 XAH 0.46875 0.722892
153 MYR AMP 0.468085 0.722892
154 KB1 0.468085 0.8
155 ACK 0.467532 0.753425
156 QQY 0.467532 0.76
157 RP1 0.467532 0.810811
158 SP1 0.467532 0.810811
159 ADP BMA 0.467391 0.789474
160 MTP 0.464789 0.767123
161 3L1 0.464789 0.814286
162 3D1 0.464789 0.814286
163 9SN 0.463158 0.75
164 A A 0.462366 0.810811
165 PPS 0.45977 0.731707
166 PAP 0.458824 0.773333
167 26A 0.458333 0.777778
168 2FA 0.458333 0.805556
169 FA5 0.458333 0.779221
170 YAP 0.458333 0.769231
171 BIS 0.457447 0.7375
172 JB6 0.457447 0.805195
173 FYA 0.457447 0.8
174 NOC 0.457143 0.779412
175 CMP 0.45679 0.816901
176 2BA 0.45679 0.805556
177 YSA 0.453608 0.729412
178 VRT 0.453488 0.783784
179 SO8 0.453488 0.805556
180 25L 0.452632 0.8
181 5F1 0.452055 0.797101
182 TAD 0.45 0.7625
183 4UV 0.44898 0.769231
184 V3L 0.448276 0.786667
185 ARG AMP 0.445545 0.694118
186 LAQ 0.445545 0.7875
187 7D3 0.444444 0.730769
188 7C5 0.444444 0.786667
189 TT8 0.444444 0.833333
190 ATP A A A 0.443299 0.821918
191 NVA 2AD 0.44186 0.756757
192 LPA AMP 0.441176 0.7875
193 7MD 0.44 0.702381
194 4UU 0.44 0.769231
195 D3Y 0.43956 0.830986
196 1DA 0.438356 0.865672
197 6MD 0.438356 0.826087
198 NAI 0.436893 0.759494
199 NAX 0.436893 0.731707
200 KH3 0.435644 0.746835
201 4YB 0.435644 0.712644
202 AMP DBH 0.434343 0.789474
203 AHZ 0.431373 0.722892
204 2A5 0.430233 0.721519
205 G3A 0.43 0.75
206 J1A 0.428571 0.753086
207 48N 0.427184 0.728395
208 YLP 0.427184 0.705882
209 G5P 0.425743 0.75
210 AR6 AR6 0.425743 0.810811
211 AFH 0.425743 0.740741
212 ATR 0.425287 0.76
213 7D4 0.423529 0.730769
214 DND 0.423077 0.779221
215 TXD 0.423077 0.759494
216 6V0 0.423077 0.75
217 4UW 0.423077 0.740741
218 NXX 0.423077 0.779221
219 GTA 0.421569 0.722892
220 IOT 0.420561 0.697674
221 TXE 0.419048 0.759494
222 LA8 ALF 3PG 0.419048 0.719512
223 TYM 0.419048 0.779221
224 AF3 ADP 3PG 0.419048 0.719512
225 OMR 0.419048 0.714286
226 649 0.419048 0.715909
227 WSA 0.419048 0.738095
228 ALF ADP 3PG 0.419048 0.719512
229 3NZ 0.416667 0.797297
230 J1C 0.415254 0.663043
231 7MC 0.415094 0.686047
232 YLB 0.415094 0.705882
233 YLC 0.415094 0.722892
234 J1B 0.413793 0.663043
235 A2R 0.413043 0.776316
236 CNA 0.412844 0.779221
237 UP5 0.409524 0.769231
238 101 0.407407 0.75
239 PGS 0.406977 0.7375
240 A A A 0.40625 0.8
241 ADJ 0.40367 0.73494
242 YLA 0.40367 0.705882
243 D5M 0.402439 0.75
244 DA 0.402439 0.75
245 AP0 0.401869 0.75
246 4TC 0.401869 0.75
247 UPA 0.401869 0.759494
248 DZD 0.401786 0.7625
249 IVH 0.4 0.75641
250 ARJ 0.4 0.764706
251 BS5 0.4 0.688889
252 AYB 0.4 0.697674
253 AFX 0.4 0.689189
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
Feedback