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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: 264
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 RAB 0.741379 0.865672
8 XYA 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 LMS 0.637681 0.753086
19 AMP 0.637681 0.808219
20 A 0.637681 0.808219
21 SRA 0.628571 0.813333
22 ZAS 0.614286 0.830986
23 J7C 0.611111 0.783784
24 AAT 0.607595 0.810811
25 6RE 0.605634 0.773333
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 GJV 0.581081 0.763158
33 S4M 0.581081 0.759494
34 SON 0.578947 0.779221
35 SXZ 0.574713 0.789474
36 AP2 0.573333 0.779221
37 MAO 0.573333 0.75
38 BA3 0.573333 0.810811
39 A12 0.573333 0.779221
40 ADX 0.571429 0.753086
41 CA0 0.571429 0.766234
42 5AS 0.565789 0.709302
43 B4P 0.565789 0.810811
44 ADP 0.565789 0.786667
45 AP5 0.565789 0.810811
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 AT4 0.558442 0.802632
52 M33 0.551282 0.776316
53 AU1 0.551282 0.766234
54 MHZ 0.551282 0.75
55 SA8 0.55 0.786667
56 EEM 0.548781 0.766234
57 ACP 0.544304 0.766234
58 ATP 0.544304 0.786667
59 HEJ 0.544304 0.786667
60 SAI 0.54321 0.819444
61 G5A 0.54321 0.709302
62 APR 0.5375 0.786667
63 PRX 0.5375 0.766234
64 AR6 0.5375 0.786667
65 AQP 0.5375 0.786667
66 5FA 0.5375 0.786667
67 APC 0.5375 0.779221
68 GAP 0.536585 0.766234
69 SAM 0.536585 0.789474
70 SRP 0.535714 0.75641
71 SMM 0.535714 0.759494
72 3AM 0.534247 0.77027
73 NEC 0.533333 0.785714
74 A3G 0.533333 0.816901
75 SAP 0.530864 0.792208
76 ADP PO3 0.530864 0.808219
77 ADV 0.530864 0.779221
78 AD9 0.530864 0.766234
79 AGS 0.530864 0.792208
80 RBY 0.530864 0.779221
81 5AL 0.53012 0.776316
82 A5A 0.52381 0.73494
83 ANP 0.518072 0.766234
84 TAT 0.518072 0.802632
85 ACQ 0.518072 0.766234
86 T99 0.518072 0.802632
87 S7M 0.517647 0.789474
88 SSA 0.517647 0.709302
89 VO4 ADP 0.517647 0.776316
90 ADP VO4 0.517647 0.776316
91 8QN 0.517241 0.776316
92 A3P 0.512821 0.783784
93 52H 0.511628 0.709302
94 VMS 0.511628 0.717647
95 54H 0.511628 0.717647
96 3AD 0.507246 0.850746
97 7D5 0.506849 0.75
98 ALF ADP 0.505882 0.746835
99 ADP ALF 0.505882 0.746835
100 ATF 0.505882 0.75641
101 TSB 0.505747 0.72619
102 DAL AMP 0.505747 0.776316
103 8X1 0.505747 0.685393
104 5CA 0.505747 0.709302
105 53H 0.505747 0.709302
106 AHX 0.505618 0.728395
107 00A 0.505618 0.759494
108 NVA LMS 0.505618 0.685393
109 25A 0.5 0.810811
110 GEK 0.5 0.821918
111 9ZA 0.5 0.7375
112 OOB 0.5 0.8
113 6YZ 0.5 0.766234
114 LEU LMS 0.5 0.685393
115 9ZD 0.5 0.7375
116 A3S 0.5 0.828571
117 3UK 0.5 0.789474
118 2AM 0.5 0.76
119 0UM 0.494382 0.776316
120 NSS 0.494382 0.709302
121 4AD 0.494382 0.746835
122 LSS 0.494382 0.693182
123 AMO 0.494382 0.75641
124 DSZ 0.494382 0.709302
125 PAJ 0.494382 0.719512
126 CC5 0.492537 0.863636
127 ME8 0.48913 0.722892
128 DLL 0.488889 0.8
129 62X 0.488889 0.7375
130 MAP 0.488636 0.746835
131 A22 0.488636 0.8
132 A3T 0.487805 0.84058
133 OAD 0.483516 0.766234
134 K15 0.483516 0.75641
135 5SV 0.483146 0.75
136 OVE 0.480519 0.776316
137 GSU 0.478261 0.709302
138 B5V 0.478261 0.779221
139 WAQ 0.478261 0.759494
140 PR8 0.478261 0.731707
141 P5A 0.478261 0.696629
142 KAA 0.478261 0.704545
143 LAD 0.478261 0.740741
144 A3R 0.477778 0.759494
145 ADQ 0.477778 0.789474
146 A1R 0.477778 0.759494
147 NVA 2AD 0.47619 0.773333
148 A2P 0.475 0.77027
149 QQX 0.473684 0.75
150 1ZZ 0.473118 0.722892
151 9K8 0.473118 0.704545
152 3OD 0.473118 0.766234
153 PTJ 0.473118 0.728395
154 TXA 0.473118 0.75641
155 NB8 0.473118 0.728395
156 2VA 0.46988 0.816901
157 XAH 0.46875 0.722892
158 KB1 0.468085 0.8
159 MYR AMP 0.468085 0.722892
160 QQY 0.467532 0.76
161 ACK 0.467532 0.753425
162 RP1 0.467532 0.810811
163 SP1 0.467532 0.810811
164 9X8 0.467391 0.769231
165 ADP BMA 0.467391 0.789474
166 MTP 0.464789 0.767123
167 3D1 0.464789 0.814286
168 3L1 0.464789 0.814286
169 9SN 0.463158 0.75
170 A A 0.462366 0.810811
171 PPS 0.45977 0.731707
172 PAP 0.458824 0.773333
173 26A 0.458333 0.777778
174 B5Y 0.458333 0.769231
175 B5M 0.458333 0.769231
176 FA5 0.458333 0.779221
177 2FA 0.458333 0.805556
178 8PZ 0.458333 0.729412
179 YAP 0.458333 0.769231
180 BIS 0.457447 0.7375
181 JB6 0.457447 0.805195
182 FYA 0.457447 0.8
183 NOC 0.457143 0.779412
184 CMP 0.45679 0.816901
185 2BA 0.45679 0.805556
186 YSA 0.453608 0.729412
187 SO8 0.453488 0.805556
188 VRT 0.453488 0.783784
189 25L 0.452632 0.8
190 5F1 0.452055 0.797101
191 TAD 0.45 0.7625
192 TYR AMP 0.44898 0.769231
193 4UV 0.44898 0.769231
194 V3L 0.448276 0.786667
195 LAQ 0.445545 0.7875
196 7C5 0.444444 0.786667
197 TT8 0.444444 0.833333
198 7D3 0.444444 0.730769
199 ATP A A A 0.443299 0.821918
200 LPA AMP 0.441176 0.7875
201 ARG AMP 0.44 0.694118
202 7MD 0.44 0.702381
203 4UU 0.44 0.769231
204 D3Y 0.43956 0.830986
205 1DA 0.438356 0.865672
206 6MD 0.438356 0.826087
207 NAX 0.436893 0.731707
208 NAI 0.436893 0.759494
209 DQV 0.435644 0.8
210 KH3 0.435644 0.746835
211 4YB 0.435644 0.712644
212 AMP DBH 0.434343 0.789474
213 AHZ 0.431373 0.722892
214 2A5 0.430233 0.721519
215 G3A 0.43 0.75
216 F0P 0.428571 0.810811
217 J1A 0.428571 0.753086
218 8Q2 0.428571 0.704545
219 48N 0.427184 0.728395
220 YLP 0.427184 0.705882
221 AR6 AR6 0.425743 0.810811
222 AFH 0.425743 0.740741
223 G5P 0.425743 0.75
224 GA7 0.425743 0.779221
225 ATR 0.425287 0.76
226 7D4 0.423529 0.730769
227 TXD 0.423077 0.759494
228 6V0 0.423077 0.75
229 NXX 0.423077 0.779221
230 4UW 0.423077 0.740741
231 DND 0.423077 0.779221
232 GTA 0.421569 0.722892
233 IOT 0.420561 0.697674
234 WSA 0.419048 0.738095
235 AF3 ADP 3PG 0.419048 0.719512
236 TYM 0.419048 0.779221
237 649 0.419048 0.715909
238 TXE 0.419048 0.759494
239 OMR 0.419048 0.714286
240 3NZ 0.416667 0.797297
241 J1C 0.415254 0.663043
242 YLC 0.415094 0.722892
243 YLB 0.415094 0.705882
244 7MC 0.415094 0.686047
245 J1B 0.413793 0.663043
246 A2R 0.413043 0.776316
247 CNA 0.412844 0.779221
248 UP5 0.409524 0.769231
249 101 0.407407 0.75
250 PGS 0.406977 0.7375
251 A A A 0.40625 0.8
252 ADJ 0.40367 0.73494
253 YLA 0.40367 0.705882
254 D5M 0.402439 0.75
255 DA 0.402439 0.75
256 AP0 0.401869 0.75
257 4TC 0.401869 0.75
258 UPA 0.401869 0.759494
259 DZD 0.401786 0.7625
260 IVH 0.4 0.75641
261 AFX 0.4 0.689189
262 AYB 0.4 0.697674
263 ARJ 0.4 0.764706
264 BS5 0.4 0.688889
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: 34
This union binding pocket(no: 1) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
1 6C74 PC None
2 3ZW2 NAG GAL FUC None
3 1SJN DUP 1.17647
4 6BMS POV 1.83824
5 6BR8 6OU 2.20588
6 3B6C SDN 2.5641
7 4WBD CIT 3.67647
8 1V2A GTS 3.80952
9 1M2Z BOG 3.89105
10 5TQZ GLC 4
11 3HCH RSM 4.10959
12 4NTO 1PW 4.34783
13 2D3Y DU 4.41176
14 4CSD MFU 4.41176
15 5YLF BGC 4.77941
16 1DJ9 KAM 4.77941
17 4OAS 2SW 5.20833
18 2VAR ANP 5.51471
19 2Z3U CRR 5.88235
20 1PFK ADP 5.88235
21 3KO0 TFP 5.94059
22 3W6X HZP 6.11354
23 5FPE 3TR 6.25
24 3SAO DBH 6.875
25 2DUR MAN MAN 8.3004
26 6FA4 D1W 8.67052
27 5TXR PLP 9.55882
28 3V2U ATP 10.2941
29 3SE5 ANP 10.3659
30 4LWU 20U 10.5882
31 3ZC7 ATP 11.1111
32 2VL1 GLY GLY 11.3971
33 4G86 BNT 12.8676
34 1LNX URI 37.037
Pocket No.: 2; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 5dhu.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2PNC CLU 2.94118
2 3ZO7 K6H 7.44681
3 2WR9 MAN MAN 7.8125
4 4OHU NAD 8.08823
5 4OHU 2TK 8.08823
6 1APZ ASP 8.51064
Pocket No.: 3; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 5dhu.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO4 PIH None
2 4Z87 GDP 2.20588
3 5T2U NAP 2.41935
4 3VZS CAA 3.11284
5 3VZS NAP 3.11284
6 4GID 0GH 4.77941
7 2B6N ALA PRO THR 5.39568
8 5A5W GUO 10.2767
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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