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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: 280
No: Ligand ECFP6 Tc MDL keys Tc
1 AOC 1 1
2 LMS 0.666667 0.740741
3 A 0.666667 0.84507
4 AMP 0.666667 0.84507
5 RAB 0.661538 0.907692
6 XYA 0.661538 0.907692
7 ADN 0.661538 0.907692
8 SRA 0.657534 0.8
9 SON 0.649351 0.789474
10 5N5 0.641791 0.878788
11 ABM 0.64 0.821918
12 A2D 0.64 0.821918
13 A3N 0.64 0.924242
14 5CD 0.632353 0.892308
15 A4D 0.632353 0.878788
16 AP2 0.623377 0.789474
17 BA3 0.623377 0.821918
18 A12 0.623377 0.789474
19 AU1 0.620253 0.8
20 AP5 0.615385 0.821918
21 B4P 0.615385 0.821918
22 5AS 0.615385 0.697674
23 ADP 0.615385 0.821918
24 AT4 0.607595 0.789474
25 AN2 0.607595 0.810811
26 EP4 0.605634 0.855072
27 ADX 0.6 0.740741
28 M33 0.6 0.810811
29 CA0 0.6 0.8
30 DTA 0.597222 0.84058
31 M2T 0.597222 0.830986
32 3DH 0.594595 0.880597
33 ACP 0.592593 0.8
34 50T 0.592593 0.810811
35 ATP 0.592593 0.821918
36 HEJ 0.592593 0.821918
37 MTA 0.589041 0.880597
38 AR6 0.585366 0.821918
39 PRX 0.585366 0.8
40 AQP 0.585366 0.821918
41 5FA 0.585366 0.821918
42 APR 0.585366 0.821918
43 APC 0.585366 0.789474
44 ADV 0.578313 0.789474
45 AGS 0.578313 0.779221
46 SAP 0.578313 0.779221
47 ADP PO3 0.578313 0.84507
48 AD9 0.578313 0.8
49 RBY 0.578313 0.789474
50 G5A 0.571429 0.697674
51 ADP ALF 0.569767 0.779221
52 ALF ADP 0.569767 0.779221
53 T99 0.564706 0.789474
54 TAT 0.564706 0.789474
55 GAP 0.564706 0.8
56 ACQ 0.564706 0.8
57 ANP 0.564706 0.8
58 OOB 0.561798 0.810811
59 5AD 0.558824 0.828125
60 ZAS 0.558442 0.816901
61 5AL 0.55814 0.810811
62 ATF 0.551724 0.789474
63 A5A 0.551724 0.722892
64 6RE 0.551282 0.783784
65 DAL AMP 0.550562 0.810811
66 8X1 0.550562 0.674157
67 6YZ 0.545455 0.8
68 VO4 ADP 0.545455 0.810811
69 ADP VO4 0.545455 0.810811
70 SRP 0.545455 0.789474
71 SSA 0.545455 0.697674
72 5SV 0.544444 0.759494
73 DSH 0.544304 0.819444
74 MAO 0.54321 0.782051
75 VMS 0.539326 0.705882
76 54H 0.539326 0.705882
77 52H 0.539326 0.697674
78 PAJ 0.538462 0.75
79 ADQ 0.538462 0.8
80 B5V 0.537634 0.789474
81 J7C 0.5375 0.794521
82 MAP 0.533333 0.779221
83 TSB 0.533333 0.714286
84 A22 0.533333 0.810811
85 53H 0.533333 0.697674
86 5CA 0.533333 0.697674
87 00A 0.532609 0.769231
88 DLL 0.532609 0.810811
89 1ZZ 0.531915 0.731707
90 GJV 0.530864 0.773333
91 S4M 0.530864 0.746835
92 7D7 0.528571 0.820895
93 9ZD 0.527473 0.769231
94 25A 0.527473 0.821918
95 9ZA 0.527473 0.769231
96 8QN 0.527473 0.810811
97 ADP BMA 0.526882 0.8
98 3UK 0.526882 0.8
99 MYR AMP 0.526316 0.731707
100 AMO 0.521739 0.789474
101 LSS 0.521739 0.681818
102 A3R 0.521739 0.769231
103 A1R 0.521739 0.769231
104 DSZ 0.521739 0.697674
105 4AD 0.521739 0.779221
106 NSS 0.521739 0.697674
107 WAQ 0.521277 0.769231
108 A A 0.521277 0.821918
109 GSU 0.521277 0.697674
110 P5A 0.521277 0.666667
111 AMP DBH 0.520408 0.8
112 SFG 0.517647 0.826087
113 5X8 0.517647 0.867647
114 NVA LMS 0.516129 0.674157
115 AHX 0.516129 0.759494
116 3OD 0.515789 0.8
117 FYA 0.515789 0.810811
118 9K8 0.515789 0.674157
119 PTJ 0.515789 0.759494
120 7C5 0.515152 0.821918
121 A7D 0.511905 0.882353
122 9X8 0.510638 0.779221
123 OAD 0.510638 0.8
124 LEU LMS 0.510638 0.674157
125 8Q2 0.509615 0.712644
126 Y3J 0.506849 0.80303
127 3AM 0.506329 0.805556
128 MHZ 0.505882 0.7375
129 A5D 0.505747 0.84058
130 LAD 0.505263 0.75
131 KAA 0.505263 0.674157
132 PR8 0.505263 0.740741
133 9SN 0.505155 0.759494
134 ME8 0.5 0.753086
135 NB8 0.5 0.759494
136 FA5 0.5 0.789474
137 TXA 0.5 0.789474
138 BIS 0.5 0.769231
139 B5Y 0.5 0.779221
140 8PZ 0.5 0.697674
141 YAP 0.5 0.779221
142 B5M 0.5 0.779221
143 JB6 0.5 0.769231
144 ATP A A A 0.5 0.833333
145 YLA 0.495327 0.756098
146 YSA 0.494949 0.697674
147 25L 0.494845 0.810811
148 4YB 0.490196 0.681818
149 TYR AMP 0.49 0.779221
150 AAT 0.488889 0.797297
151 SA8 0.488636 0.797297
152 A3P 0.488095 0.819444
153 SAH 0.483146 0.842857
154 SAI 0.483146 0.830986
155 7D5 0.481013 0.76
156 7MD 0.480392 0.731707
157 AFH 0.480392 0.75
158 XAH 0.48 0.731707
159 SMM 0.478261 0.769231
160 SAM 0.477778 0.776316
161 NXX 0.47619 0.789474
162 NAI 0.47619 0.792208
163 DND 0.47619 0.789474
164 DQV 0.475728 0.810811
165 4UV 0.475248 0.802632
166 2AM 0.475 0.794521
167 EEM 0.472527 0.776316
168 OMR 0.471698 0.722892
169 649 0.471698 0.666667
170 LAQ 0.471154 0.731707
171 AHZ 0.471154 0.731707
172 G3A 0.470588 0.759494
173 A2P 0.470588 0.805556
174 NEC 0.46988 0.797101
175 A3G 0.46988 0.855072
176 LPA AMP 0.466667 0.731707
177 4UU 0.466019 0.802632
178 G5P 0.466019 0.759494
179 GA7 0.466019 0.789474
180 ARG AMP 0.466019 0.722892
181 AR6 AR6 0.466019 0.821918
182 CC5 0.465753 0.90625
183 S7M 0.462366 0.776316
184 GTA 0.461538 0.731707
185 TAD 0.461538 0.75
186 3AD 0.460526 0.892308
187 0UM 0.458333 0.763158
188 TXE 0.457944 0.792208
189 AF3 ADP 3PG 0.457944 0.75
190 WSA 0.457944 0.705882
191 TYM 0.457944 0.789474
192 OVE 0.457831 0.763158
193 PAP 0.455556 0.808219
194 YLB 0.453704 0.714286
195 7MC 0.453704 0.714286
196 48N 0.45283 0.759494
197 YLP 0.45283 0.714286
198 A6D 0.44898 0.74359
199 K15 0.44898 0.766234
200 UP5 0.448598 0.802632
201 4UW 0.448598 0.772152
202 NAX 0.448598 0.7625
203 TXD 0.448598 0.815789
204 6V0 0.448598 0.782051
205 GEK 0.447917 0.808219
206 S8M 0.447917 0.808219
207 QQY 0.445783 0.723684
208 V3L 0.445652 0.821918
209 2A5 0.444444 0.753247
210 SLU 0.443478 0.689655
211 A3S 0.443182 0.867647
212 NAD 0.442478 0.810811
213 7D3 0.44186 0.74026
214 T5A 0.441441 0.73494
215 PPS 0.44086 0.719512
216 UPA 0.440367 0.792208
217 AP0 0.440367 0.782051
218 4TC 0.440367 0.782051
219 YLC 0.440367 0.753086
220 ATR 0.43956 0.794521
221 62X 0.438776 0.746835
222 DZD 0.438596 0.772152
223 7D4 0.438202 0.74026
224 CNA 0.4375 0.789474
225 A4P 0.436364 0.717647
226 KB1 0.435644 0.786667
227 A3D 0.434783 0.8
228 QQX 0.433735 0.714286
229 A3T 0.433333 0.880597
230 IOT 0.432432 0.705882
231 IMO 0.430233 0.780822
232 4TA 0.429825 0.743902
233 G A A A 0.429825 0.759494
234 COD 0.429825 0.689655
235 AMP NAD 0.429825 0.810811
236 SP1 0.428571 0.75
237 RP1 0.428571 0.75
238 ADJ 0.428571 0.765432
239 ACK 0.428571 0.763889
240 139 0.428571 0.7625
241 A2R 0.427083 0.810811
242 BT5 0.426087 0.705882
243 SXZ 0.425743 0.776316
244 EO7 0.425287 0.705882
245 AYB 0.424779 0.705882
246 M24 0.423729 0.740741
247 MTP 0.423077 0.777778
248 3D1 0.423077 0.826087
249 3L1 0.423077 0.826087
250 80F 0.422414 0.73494
251 F2R 0.421053 0.714286
252 2BA 0.420455 0.791667
253 CMP 0.420455 0.802817
254 NAE 0.420168 0.779221
255 PO4 PO4 A A A A PO4 0.42 0.805556
256 A A A 0.42 0.810811
257 NAJ PZO 0.418803 0.782051
258 2FA 0.417722 0.842857
259 26A 0.417722 0.84058
260 2VA 0.417582 0.855072
261 A G 0.417391 0.769231
262 BTX 0.417391 0.714286
263 NAQ 0.416667 0.759494
264 U A G G 0.413793 0.769231
265 ZID 0.413223 0.8
266 5F1 0.4125 0.782609
267 YLY 0.411765 0.705882
268 D3Y 0.408163 0.842857
269 KH3 0.407407 0.75641
270 U A 0.40678 0.792208
271 PGS 0.406593 0.725
272 ITT 0.406593 0.77027
273 NA7 0.405941 0.789474
274 NDE 0.404762 0.789474
275 SO8 0.404255 0.842857
276 3NZ 0.401961 0.833333
277 F0P 0.401786 0.797297
278 3AT 0.4 0.797297
279 1DA 0.4 0.907692
280 6MD 0.4 0.865672
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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