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Receptor
PDB id Resolution Class Description Source Keywords
3V7U 1.97 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH MTA 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...
MTA A:301;
A:302;
Valid;
Valid;
none;
none;
submit data
297.334 C11 H15 N5 O3 S CSC[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: MTA; Similar ligands found: 267
No: Ligand ECFP6 Tc MDL keys Tc
1 MTA 1 1
2 DTA 0.786885 0.867647
3 3DH 0.777778 0.938462
4 ADN 0.758621 0.878788
5 RAB 0.758621 0.878788
6 XYA 0.758621 0.878788
7 DSH 0.705882 0.84507
8 5N5 0.704918 0.878788
9 A4D 0.693548 0.907692
10 5CD 0.693548 0.892308
11 EP4 0.6875 0.939394
12 M2T 0.676923 0.940298
13 A7D 0.657534 0.882353
14 5X8 0.64 0.895522
15 5AD 0.639344 0.857143
16 AMP 0.628571 0.794521
17 A 0.628571 0.794521
18 ZAS 0.628571 0.816901
19 LMS 0.628571 0.719512
20 A5D 0.623377 0.867647
21 SAH 0.615385 0.869565
22 ABM 0.60274 0.821918
23 J7C 0.60274 0.794521
24 AAT 0.6 0.797297
25 6RE 0.597222 0.783784
26 SRA 0.597222 0.776316
27 S4M 0.594595 0.84
28 AOC 0.589041 0.880597
29 MAO 0.586667 0.805195
30 S8M 0.583333 0.833333
31 A2D 0.581081 0.773333
32 A3N 0.581081 0.867647
33 5AS 0.578947 0.697674
34 GJV 0.573333 0.773333
35 A12 0.565789 0.74359
36 AP2 0.565789 0.74359
37 BA3 0.565789 0.773333
38 AU1 0.564103 0.753247
39 ADX 0.564103 0.719512
40 M33 0.564103 0.810811
41 MHZ 0.564103 0.805195
42 B4P 0.558442 0.773333
43 AP5 0.558442 0.773333
44 ADP 0.558442 0.773333
45 7D7 0.553846 0.794118
46 Y3J 0.552239 0.80303
47 AN2 0.551282 0.763158
48 AT4 0.551282 0.766234
49 SON 0.551282 0.74359
50 SXZ 0.550562 0.849315
51 PRX 0.55 0.8
52 A6D 0.545455 0.766234
53 CA0 0.544304 0.753247
54 AD9 0.54321 0.753247
55 SA8 0.54321 0.873239
56 EEM 0.542169 0.849315
57 ACP 0.5375 0.753247
58 SFG 0.5375 0.826087
59 50T 0.5375 0.763158
60 HEJ 0.5375 0.773333
61 ATP 0.5375 0.773333
62 5FA 0.530864 0.773333
63 AQP 0.530864 0.773333
64 APC 0.530864 0.74359
65 APR 0.530864 0.773333
66 AR6 0.530864 0.773333
67 ANP 0.53012 0.753247
68 SAM 0.53012 0.875
69 SMM 0.529412 0.84
70 3AM 0.527027 0.756757
71 NEC 0.526316 0.823529
72 RBY 0.52439 0.74359
73 AGS 0.52439 0.75641
74 SAP 0.52439 0.75641
75 ADP PO3 0.52439 0.794521
76 ADV 0.52439 0.74359
77 5AL 0.52381 0.786667
78 54H 0.523256 0.705882
79 VMS 0.523256 0.705882
80 3AD 0.521739 0.863636
81 MTH 0.520548 0.984127
82 G5A 0.518072 0.678161
83 SAI 0.518072 0.830986
84 A5A 0.517647 0.722892
85 ME8 0.516484 0.797468
86 GAP 0.511905 0.753247
87 ACQ 0.511905 0.753247
88 T99 0.511905 0.766234
89 TAT 0.511905 0.766234
90 S7M 0.511628 0.824324
91 8QN 0.511364 0.786667
92 9ZD 0.511364 0.769231
93 9ZA 0.511364 0.769231
94 CC5 0.507463 0.876923
95 A3G 0.506494 0.828571
96 A3P 0.506329 0.77027
97 52H 0.505747 0.697674
98 NVA LMS 0.5 0.693182
99 7D5 0.5 0.714286
100 8X1 0.5 0.655556
101 53H 0.5 0.697674
102 ALF ADP 0.5 0.734177
103 ATF 0.5 0.74359
104 TSB 0.5 0.714286
105 MTP 0.5 0.828571
106 MAP 0.5 0.734177
107 ADP ALF 0.5 0.734177
108 DAL AMP 0.5 0.786667
109 25A 0.494382 0.773333
110 5SV 0.494382 0.759494
111 VO4 ADP 0.494253 0.763158
112 6YZ 0.494253 0.753247
113 ADP VO4 0.494253 0.763158
114 SRP 0.494253 0.74359
115 SSA 0.494253 0.678161
116 2AM 0.493333 0.746667
117 26A 0.492958 0.867647
118 PAJ 0.488889 0.75
119 LSS 0.488889 0.701149
120 A1R 0.488889 0.725
121 DSZ 0.488889 0.678161
122 ADQ 0.488889 0.753247
123 0UM 0.488889 0.810811
124 A3R 0.488889 0.725
125 3OD 0.483871 0.776316
126 AHX 0.483516 0.716049
127 62X 0.483516 0.815789
128 5CA 0.483146 0.678161
129 A22 0.483146 0.763158
130 A3T 0.481928 0.880597
131 2VA 0.481928 0.855072
132 RP1 0.480519 0.75
133 SP1 0.480519 0.75
134 3L1 0.478873 0.8
135 3D1 0.478873 0.8
136 OAD 0.478261 0.776316
137 LEU LMS 0.478261 0.693182
138 9X8 0.478261 0.779221
139 K15 0.478261 0.813333
140 OOB 0.477778 0.763158
141 GEK 0.477778 0.833333
142 A3S 0.47561 0.84058
143 OVE 0.474359 0.74026
144 P5A 0.473118 0.648352
145 PR8 0.473118 0.698795
146 NSS 0.472527 0.678161
147 4AD 0.472527 0.734177
148 AMO 0.472527 0.74359
149 2FA 0.472222 0.816901
150 6MD 0.472222 0.893939
151 NOC 0.471429 0.791045
152 NVA 2AD 0.470588 0.833333
153 A2P 0.469136 0.756757
154 2BA 0.469136 0.767123
155 CMP 0.469136 0.777778
156 9K8 0.468085 0.674157
157 PTJ 0.468085 0.759494
158 TXA 0.468085 0.766234
159 1ZZ 0.468085 0.731707
160 QQX 0.467532 0.714286
161 DLL 0.467391 0.763158
162 00A 0.467391 0.725
163 5F1 0.465753 0.782609
164 MYR AMP 0.463158 0.731707
165 3UK 0.462366 0.753247
166 ADP BMA 0.462366 0.753247
167 QQY 0.461538 0.723684
168 ACK 0.461538 0.739726
169 WAQ 0.457447 0.725
170 LAD 0.457447 0.707317
171 A A 0.457447 0.773333
172 B5V 0.457447 0.74359
173 GSU 0.457447 0.678161
174 KAA 0.457447 0.655556
175 PPS 0.454545 0.698795
176 B5Y 0.453608 0.75641
177 B5M 0.453608 0.75641
178 PAP 0.453488 0.76
179 BIS 0.452632 0.725
180 JB6 0.452632 0.746835
181 NB8 0.452632 0.716049
182 FYA 0.452632 0.763158
183 1DA 0.452055 0.878788
184 XAH 0.44898 0.690476
185 SO8 0.448276 0.869565
186 VRT 0.448276 0.84507
187 25L 0.447917 0.763158
188 KB1 0.447917 0.786667
189 4UV 0.444444 0.734177
190 9SN 0.443299 0.716049
191 V3L 0.443182 0.773333
192 LAQ 0.441176 0.710843
193 7D3 0.439024 0.696203
194 FA5 0.438776 0.74359
195 YAP 0.438776 0.734177
196 ATP A A A 0.438776 0.783784
197 8PZ 0.438776 0.678161
198 J1A 0.4375 0.740741
199 LPA AMP 0.436893 0.710843
200 J1C 0.435897 0.67033
201 7MD 0.435644 0.690476
202 AFH 0.435644 0.707317
203 GA7 0.435644 0.789474
204 4UU 0.435644 0.734177
205 J1B 0.434783 0.67033
206 YSA 0.434343 0.678161
207 4UW 0.432692 0.75
208 TXD 0.432692 0.746835
209 ARJ 0.432432 0.776119
210 MCF 0.432099 0.842857
211 GTA 0.431373 0.731707
212 TAD 0.431373 0.728395
213 KH3 0.431373 0.802632
214 4YB 0.431373 0.662921
215 TYR AMP 0.43 0.734177
216 AMP DBH 0.43 0.753247
217 IVH 0.428571 0.813333
218 AHZ 0.427184 0.731707
219 3NZ 0.427083 0.833333
220 7C5 0.425743 0.773333
221 G3A 0.425743 0.716049
222 2A5 0.425287 0.708861
223 7MC 0.424528 0.694118
224 AP0 0.424528 0.7375
225 TT8 0.423913 0.898551
226 YLP 0.423077 0.694118
227 48N 0.423077 0.7375
228 CNA 0.422018 0.74359
229 ARG AMP 0.421569 0.682353
230 AR6 AR6 0.421569 0.773333
231 G5P 0.421569 0.716049
232 ATR 0.420455 0.746667
233 101 0.419753 0.714286
234 D3Y 0.419355 0.816901
235 NXX 0.419048 0.74359
236 DND 0.419048 0.74359
237 6V0 0.419048 0.716049
238 NAX 0.419048 0.698795
239 NAI 0.419048 0.725
240 7D4 0.418605 0.696203
241 DQV 0.417476 0.763158
242 A A A 0.416667 0.763158
243 OMR 0.415094 0.722892
244 TXE 0.415094 0.725
245 649 0.415094 0.648352
246 D5M 0.414634 0.714286
247 DA 0.414634 0.714286
248 139 0.412844 0.698795
249 T5A 0.412844 0.694118
250 ADJ 0.412844 0.702381
251 YLB 0.411215 0.714286
252 YLC 0.411215 0.710843
253 F0P 0.411215 0.797297
254 8Q2 0.411215 0.655556
255 J1D 0.410714 0.628866
256 AYB 0.409091 0.705882
257 A2R 0.408602 0.763158
258 A4P 0.407407 0.659091
259 UP5 0.40566 0.734177
260 F2R 0.405405 0.674419
261 IOT 0.40367 0.666667
262 6CR 0.402597 0.805556
263 WSA 0.401869 0.686047
264 TYM 0.401869 0.74359
265 AF3 ADP 3PG 0.401869 0.707317
266 4TA 0.401786 0.702381
267 YLA 0.4 0.674419
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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