Receptor
PDB id Resolution Class Description Source Keywords
3V7W 2.01 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH 5'-AZIDO-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
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...
ZAS A:301;
A:302;
Valid;
Valid;
none;
none;
submit data
293.262 C10 H13 N8 O3 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: ZAS; Similar ligands found: 242
No: Ligand ECFP6 Tc MDL keys Tc
1 ZAS 1 1
2 ADN 0.68254 0.84058
3 XYA 0.68254 0.84058
4 RAB 0.68254 0.84058
5 5N5 0.661538 0.867647
6 5CD 0.651515 0.852941
7 A4D 0.651515 0.84058
8 MTA 0.628571 0.816901
9 EP4 0.623188 0.819444
10 DTA 0.614286 0.830986
11 M2T 0.614286 0.797297
12 3DH 0.589041 0.816901
13 A 0.573333 0.786667
14 LMS 0.573333 0.714286
15 AMP 0.573333 0.786667
16 6RE 0.565789 0.849315
17 SRA 0.565789 0.746835
18 AOC 0.558442 0.816901
19 DSH 0.558442 0.810811
20 5AD 0.552239 0.791045
21 45A 0.551282 0.766234
22 J7C 0.551282 0.835616
23 A2D 0.551282 0.766234
24 ABM 0.551282 0.766234
25 A3N 0.551282 0.830986
26 ADP 0.55 0.766234
27 S4M 0.544304 0.7625
28 GJV 0.544304 0.837838
29 7D7 0.544118 0.760563
30 BA3 0.5375 0.766234
31 AP2 0.5375 0.7375
32 MAO 0.5375 0.775
33 A12 0.5375 0.7375
34 ADX 0.536585 0.694118
35 AP5 0.530864 0.766234
36 5AS 0.530864 0.693182
37 B4P 0.530864 0.766234
38 SFG 0.53012 0.816901
39 ADP MG 0.52439 0.810811
40 AT4 0.52439 0.7375
41 A7D 0.52439 0.794521
42 SON 0.52439 0.7375
43 AN2 0.52439 0.779221
44 Y3J 0.521127 0.768116
45 CA0 0.518072 0.746835
46 MHZ 0.518072 0.797468
47 AU1 0.518072 0.792208
48 M33 0.518072 0.75641
49 Z8B 0.5125 0.916667
50 ACP 0.511905 0.746835
51 50T 0.511905 0.75641
52 HEJ 0.511905 0.766234
53 H1Q 0.511905 0.8
54 5X8 0.511905 0.830986
55 KG4 0.511905 0.746835
56 ATP 0.511905 0.766234
57 AR6 0.505882 0.766234
58 AQP 0.505882 0.766234
59 PRX 0.505882 0.746835
60 APR 0.505882 0.766234
61 APC 0.505882 0.7375
62 5FA 0.505882 0.766234
63 ADP PO3 0.5 0.810811
64 APC MG 0.5 0.789474
65 3AM 0.5 0.75
66 AD9 0.5 0.746835
67 RBY 0.5 0.7375
68 A5D 0.5 0.830986
69 AGS 0.5 0.728395
70 A3G 0.5 0.84507
71 ATP MG 0.5 0.810811
72 SA8 0.5 0.789474
73 EEM 0.5 0.769231
74 ADV 0.5 0.7375
75 SAP 0.5 0.728395
76 ATF 0.494382 0.7375
77 SAH 0.494253 0.808219
78 G5A 0.494253 0.712644
79 SAI 0.494253 0.797297
80 SAM 0.488636 0.769231
81 ACQ 0.488636 0.746835
82 TAT 0.488636 0.7375
83 GAP 0.488636 0.792208
84 ANP 0.488636 0.792208
85 T99 0.488636 0.7375
86 ADQ 0.483871 0.746835
87 HQG 0.483516 0.75641
88 5AL 0.483146 0.75641
89 AAT 0.483146 0.789474
90 8LE 0.483146 0.728395
91 NEC 0.481481 0.788732
92 A5A 0.477778 0.697674
93 ALF ADP 0.477778 0.75
94 ADP ALF 0.477778 0.75
95 7D5 0.474359 0.708861
96 GEK 0.473118 0.8
97 8QN 0.473118 0.75641
98 3AD 0.472973 0.826087
99 6YZ 0.472527 0.746835
100 SMM 0.472527 0.740741
101 S7M 0.472527 0.769231
102 SRP 0.472527 0.759494
103 SSA 0.472527 0.693182
104 8LH 0.472527 0.7375
105 VO4 ADP 0.472527 0.779221
106 ADP VO4 0.472527 0.779221
107 A3S 0.470588 0.830986
108 2AM 0.468354 0.74026
109 PAJ 0.468085 0.702381
110 54H 0.467391 0.681818
111 52H 0.467391 0.674157
112 VMS 0.467391 0.681818
113 A3P 0.464286 0.763158
114 N5O 0.463415 0.805556
115 62X 0.463158 0.740741
116 8X1 0.462366 0.688889
117 53H 0.462366 0.674157
118 8LQ 0.462366 0.7375
119 TSB 0.462366 0.689655
120 5CA 0.462366 0.693182
121 A22 0.462366 0.75641
122 DAL AMP 0.462366 0.779221
123 MAP 0.462366 0.772152
124 A3T 0.45977 0.816901
125 KB1 0.459184 0.779221
126 ADP BMA 0.458333 0.769231
127 CC5 0.458333 0.838235
128 K15 0.458333 0.759494
129 S8M 0.457447 0.875
130 25A 0.457447 0.766234
131 5SV 0.457447 0.710843
132 OZV 0.457447 0.766234
133 OOB 0.457447 0.75641
134 9ZA 0.457447 0.740741
135 9ZD 0.457447 0.740741
136 QQY 0.45679 0.696203
137 GSU 0.453608 0.693182
138 B5V 0.453608 0.7375
139 3D1 0.453333 0.791667
140 3L1 0.453333 0.791667
141 A3R 0.452632 0.7625
142 0UM 0.452632 0.779221
143 NSS 0.452632 0.712644
144 A1R 0.452632 0.7625
145 DSZ 0.452632 0.693182
146 AMO 0.452632 0.759494
147 LSS 0.452632 0.677778
148 4AD 0.452632 0.772152
149 7D3 0.452381 0.691358
150 N5A 0.452381 0.802817
151 OVE 0.451219 0.7125
152 PAP 0.449438 0.753247
153 BIS 0.44898 0.719512
154 9K8 0.44898 0.634409
155 ME8 0.44898 0.705882
156 NVA LMS 0.447917 0.688889
157 AHX 0.447917 0.753086
158 00A 0.447917 0.719512
159 DLL 0.447917 0.75641
160 QQX 0.444444 0.6875
161 A6D 0.443299 0.828947
162 3UK 0.443299 0.746835
163 LEU LMS 0.443299 0.688889
164 OAD 0.443299 0.746835
165 9X8 0.443299 0.728395
166 5F1 0.441558 0.774648
167 RP1 0.439024 0.721519
168 ACK 0.439024 0.733333
169 SP1 0.439024 0.721519
170 P5A 0.438776 0.681319
171 LAD 0.438776 0.743902
172 KAA 0.438776 0.688889
173 WAQ 0.438776 0.719512
174 PR8 0.438776 0.73494
175 A A 0.438776 0.789474
176 7C5 0.436893 0.766234
177 B5M 0.435644 0.728395
178 PPS 0.434783 0.674419
179 3OD 0.434343 0.746835
180 FYA 0.434343 0.779221
181 TXA 0.434343 0.7375
182 PTJ 0.434343 0.710843
183 NB8 0.434343 0.753086
184 1ZZ 0.434343 0.686047
185 SXZ 0.434343 0.746835
186 JB6 0.434343 0.719512
187 AFH 0.432692 0.702381
188 A2P 0.430233 0.75
189 CMP 0.430233 0.77027
190 2BA 0.430233 0.76
191 25L 0.43 0.75641
192 MYR AMP 0.43 0.705882
193 26A 0.428571 0.756757
194 2FA 0.428571 0.783784
195 KH3 0.428571 0.75
196 4UV 0.427184 0.728395
197 NOC 0.426667 0.782609
198 9SN 0.425743 0.710843
199 HZ2 0.424528 0.769231
200 V3L 0.423913 0.766234
201 2A5 0.422222 0.703704
202 YAP 0.421569 0.75
203 8PZ 0.421569 0.693182
204 B5Y 0.421569 0.728395
205 FA5 0.421569 0.759494
206 ATP A 0.421569 0.8
207 ATP A A A 0.421569 0.8
208 4UU 0.419048 0.728395
209 AR6 AR6 0.419048 0.789474
210 ARG AMP 0.419048 0.759036
211 ATR 0.417582 0.74026
212 XAH 0.417476 0.746988
213 YSA 0.417476 0.693182
214 B1U 0.417476 0.692308
215 D3Y 0.416667 0.808219
216 7D4 0.41573 0.691358
217 MTP 0.415584 0.723684
218 AMP DBH 0.413462 0.769231
219 TYR AMP 0.413462 0.772152
220 AHZ 0.411215 0.705882
221 2VA 0.411111 0.794521
222 1DA 0.410256 0.84058
223 6MD 0.410256 0.802817
224 G3A 0.409524 0.731707
225 OZP 0.407407 0.789474
226 48N 0.407407 0.731707
227 7MD 0.40566 0.746988
228 GA7 0.40566 0.7375
229 G5P 0.40566 0.731707
230 ERJ 0.404762 0.774648
231 HY8 0.40367 0.769231
232 DND 0.40367 0.759494
233 NXX 0.40367 0.759494
234 6V0 0.40367 0.731707
235 NVA 2AD 0.402174 0.8
236 DQV 0.401869 0.75641
237 TAD 0.401869 0.702381
238 GTA 0.401869 0.72619
239 4YB 0.401869 0.677778
240 101 0.4 0.730769
241 N37 0.4 0.773333
242 649 0.4 0.663043
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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