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: 256
No: Ligand ECFP6 Tc MDL keys Tc
1 MTA 1 1
2 DTA 0.786885 0.867647
3 3DH 0.777778 0.938462
4 RAB 0.758621 0.878788
5 XYA 0.758621 0.878788
6 ADN 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 ZAS 0.628571 0.816901
17 AMP 0.628571 0.794521
18 A 0.628571 0.794521
19 A5D 0.623377 0.867647
20 SAH 0.615385 0.869565
21 ABM 0.60274 0.821918
22 J7C 0.60274 0.794521
23 AAT 0.6 0.797297
24 6RE 0.597222 0.783784
25 SRA 0.597222 0.776316
26 S4M 0.594595 0.84
27 AOC 0.589041 0.880597
28 AMP MG 0.589041 0.773333
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 BA3 0.565789 0.773333
36 A12 0.565789 0.74359
37 AP2 0.565789 0.74359
38 M33 0.564103 0.810811
39 AU1 0.564103 0.753247
40 MHZ 0.564103 0.805195
41 ADX 0.564103 0.719512
42 ADP 0.558442 0.773333
43 AP5 0.558442 0.773333
44 B4P 0.558442 0.773333
45 7D7 0.553846 0.794118
46 Y3J 0.552239 0.80303
47 AN2 0.551282 0.763158
48 SON 0.551282 0.74359
49 SXZ 0.550562 0.849315
50 PRX 0.55 0.8
51 A6D 0.545455 0.766234
52 CA0 0.544304 0.753247
53 ADP MG 0.544304 0.763158
54 SA8 0.54321 0.873239
55 AD9 0.54321 0.753247
56 EEM 0.542169 0.849315
57 BEF ADP 0.5375 0.74359
58 50T 0.5375 0.763158
59 SFG 0.5375 0.826087
60 ACP 0.5375 0.753247
61 ATP 0.5375 0.773333
62 ADP BEF 0.5375 0.74359
63 AR6 0.530864 0.773333
64 APR 0.530864 0.773333
65 5FA 0.530864 0.773333
66 APC 0.530864 0.74359
67 AQP 0.530864 0.773333
68 ANP 0.53012 0.753247
69 SAM 0.53012 0.875
70 SMM 0.529412 0.84
71 3AM 0.527027 0.756757
72 NEC 0.526316 0.823529
73 RBY 0.52439 0.74359
74 SAP 0.52439 0.75641
75 AGS 0.52439 0.75641
76 ADP PO3 0.52439 0.794521
77 ADV 0.52439 0.74359
78 5AL 0.52381 0.786667
79 VMS 0.523256 0.705882
80 54H 0.523256 0.705882
81 3AD 0.521739 0.863636
82 MTH 0.520548 0.984127
83 SAI 0.518072 0.830986
84 G5A 0.518072 0.678161
85 ATP MG 0.518072 0.763158
86 A5A 0.517647 0.722892
87 ME8 0.516484 0.797468
88 ACQ 0.511905 0.753247
89 GAP 0.511905 0.753247
90 TAT 0.511905 0.766234
91 S7M 0.511628 0.824324
92 8QN 0.511364 0.786667
93 CC5 0.507463 0.876923
94 A3G 0.506494 0.828571
95 A3P 0.506329 0.77027
96 52H 0.505747 0.697674
97 MTP 0.5 0.828571
98 ADP ALF 0.5 0.734177
99 MAP 0.5 0.734177
100 TSB 0.5 0.714286
101 7D5 0.5 0.714286
102 ATF 0.5 0.74359
103 ALF ADP 0.5 0.734177
104 53H 0.5 0.697674
105 DAL AMP 0.5 0.786667
106 5SV 0.494382 0.759494
107 25A 0.494382 0.773333
108 SSA 0.494253 0.678161
109 ANP MG 0.494253 0.734177
110 ADP VO4 0.494253 0.763158
111 SRP 0.494253 0.74359
112 VO4 ADP 0.494253 0.763158
113 2AM 0.493333 0.746667
114 26A 0.492958 0.867647
115 0UM 0.488889 0.810811
116 ADQ 0.488889 0.753247
117 LSS 0.488889 0.701149
118 DSZ 0.488889 0.678161
119 PAJ 0.488889 0.75
120 A1R 0.488889 0.725
121 3OD 0.483871 0.776316
122 62X 0.483516 0.815789
123 NVA LMS 0.483516 0.701149
124 AHX 0.483516 0.716049
125 A22 0.483146 0.763158
126 5CA 0.483146 0.678161
127 A3T 0.481928 0.880597
128 2VA 0.481928 0.855072
129 RP1 0.480519 0.75
130 SP1 0.480519 0.75
131 3L1 0.478873 0.8
132 3D1 0.478873 0.8
133 OAD 0.478261 0.776316
134 K15 0.478261 0.813333
135 LEU LMS 0.478261 0.701149
136 GEK 0.477778 0.833333
137 OOB 0.477778 0.763158
138 A3S 0.47561 0.84058
139 OVE 0.474359 0.74026
140 PR8 0.473118 0.698795
141 P5A 0.473118 0.648352
142 AMO 0.472527 0.74359
143 NSS 0.472527 0.678161
144 4AD 0.472527 0.734177
145 6MD 0.472222 0.893939
146 2FA 0.472222 0.816901
147 NOC 0.471429 0.791045
148 A2P 0.469136 0.756757
149 2BA 0.469136 0.767123
150 CMP 0.469136 0.777778
151 TXA 0.468085 0.766234
152 PTJ 0.468085 0.759494
153 1ZZ 0.468085 0.731707
154 QQX 0.467532 0.714286
155 00A 0.467391 0.725
156 DLL 0.467391 0.763158
157 5F1 0.465753 0.782609
158 MYR AMP 0.463158 0.731707
159 3UK 0.462366 0.753247
160 ADP BMA 0.462366 0.753247
161 ACK 0.461538 0.739726
162 QQY 0.461538 0.723684
163 GSU 0.457447 0.678161
164 A A 0.457447 0.773333
165 WAQ 0.457447 0.725
166 LAD 0.457447 0.707317
167 KAA 0.457447 0.655556
168 PPS 0.454545 0.698795
169 PAP 0.453488 0.76
170 NVA 2AD 0.453488 0.816901
171 NB8 0.452632 0.716049
172 JB6 0.452632 0.746835
173 FYA 0.452632 0.763158
174 BIS 0.452632 0.725
175 1DA 0.452055 0.878788
176 XAH 0.44898 0.690476
177 TYR AMP 0.44898 0.74359
178 VRT 0.448276 0.84507
179 SO8 0.448276 0.869565
180 25L 0.447917 0.763158
181 KB1 0.447917 0.786667
182 4UV 0.444444 0.734177
183 9SN 0.443299 0.716049
184 V3L 0.443182 0.773333
185 LAQ 0.441176 0.710843
186 7D3 0.439024 0.696203
187 ATP A A A 0.438776 0.783784
188 FA5 0.438776 0.74359
189 YAP 0.438776 0.734177
190 J1A 0.4375 0.740741
191 LPA AMP 0.436893 0.710843
192 J1C 0.435897 0.67033
193 AFH 0.435644 0.707317
194 7MD 0.435644 0.690476
195 4UU 0.435644 0.734177
196 J1B 0.434783 0.67033
197 YSA 0.434343 0.678161
198 TXD 0.432692 0.746835
199 4UW 0.432692 0.75
200 ARJ 0.432432 0.776119
201 MCF 0.432099 0.842857
202 KH3 0.431373 0.802632
203 TAD 0.431373 0.728395
204 GTA 0.431373 0.731707
205 4YB 0.431373 0.662921
206 AMP DBH 0.43 0.753247
207 IVH 0.428571 0.813333
208 AHZ 0.427184 0.731707
209 ARG AMP 0.427184 0.682353
210 3NZ 0.427083 0.833333
211 7C5 0.425743 0.773333
212 G3A 0.425743 0.716049
213 2A5 0.425287 0.708861
214 7MC 0.424528 0.694118
215 AP0 0.424528 0.7375
216 TT8 0.423913 0.898551
217 YLP 0.423077 0.694118
218 48N 0.423077 0.7375
219 CNA 0.422018 0.74359
220 AR6 AR6 0.421569 0.773333
221 G5P 0.421569 0.716049
222 ATR 0.420455 0.746667
223 101 0.419753 0.714286
224 D3Y 0.419355 0.816901
225 NXX 0.419048 0.74359
226 NAX 0.419048 0.698795
227 DND 0.419048 0.74359
228 6V0 0.419048 0.716049
229 NAI 0.419048 0.725
230 7D4 0.418605 0.696203
231 A A A 0.416667 0.763158
232 OMR 0.415094 0.722892
233 TXE 0.415094 0.725
234 649 0.415094 0.648352
235 D5M 0.414634 0.714286
236 DA 0.414634 0.714286
237 T5A 0.412844 0.694118
238 139 0.412844 0.698795
239 ADJ 0.412844 0.702381
240 YLB 0.411215 0.714286
241 YLC 0.411215 0.710843
242 J1D 0.410714 0.628866
243 AYB 0.409091 0.705882
244 A2R 0.408602 0.763158
245 A4P 0.407407 0.659091
246 UP5 0.40566 0.734177
247 NAD IBO 0.405405 0.75641
248 IOT 0.40367 0.666667
249 6CR 0.402597 0.805556
250 WSA 0.401869 0.686047
251 TYM 0.401869 0.74359
252 LA8 ALF 3PG 0.401869 0.707317
253 ALF ADP 3PG 0.401869 0.707317
254 AF3 ADP 3PG 0.401869 0.707317
255 4TA 0.401786 0.702381
256 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: 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
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