Receptor
PDB id Resolution Class Description Source Keywords
3V7Y 1.97 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH 5'-N-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
A3N A:302;
A:303;
 Valid;
Valid;
 none;
none;
 submit data
304.305 C13 H16 N6 O3 C#CCN...
CIT A:301;
 Invalid;
 none;
 submit data
192.124 C6 H8 O7 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: A3N; Similar ligands found: 215
No: Ligand ECFP6 Tc MDL keys Tc
1 A3N 1 1
2 RAB 0.651515 0.923077
3 XYA 0.651515 0.923077
4 ADN 0.651515 0.923077
5 AOC 0.64 0.924242
6 5N5 0.632353 0.953125
7 5CD 0.623188 0.878788
8 A4D 0.623188 0.923077
9 EP4 0.597222 0.869565
10 DTA 0.589041 0.828571
11 M2T 0.589041 0.819444
12 3DH 0.586667 0.867647
13 6RE 0.584416 0.821918
14 MTA 0.581081 0.867647
15 AMP MG 0.576923 0.763158
16 A 0.571429 0.783784
17 AMP 0.571429 0.783784
18 J7C 0.56962 0.833333
19 SRA 0.564103 0.74359
20 GJV 0.5625 0.810811
21 ZAS 0.551282 0.830986
22 5AD 0.550725 0.815385
23 A2D 0.55 0.786667
24 ABM 0.55 0.763158
25 5AS 0.548781 0.689655
26 DSH 0.5375 0.859155
27 BA3 0.536585 0.786667
28 AP2 0.536585 0.75641
29 A12 0.536585 0.75641
30 ADP MG 0.535714 0.753247
31 AU1 0.535714 0.766234
32 B4P 0.53012 0.786667
33 ADP 0.53012 0.786667
34 AP5 0.53012 0.786667
35 S4M 0.52439 0.782051
36 SON 0.52381 0.734177
37 AN2 0.52381 0.776316
38 MAO 0.518072 0.75
39 CA0 0.517647 0.766234
40 ADX 0.517647 0.710843
41 M33 0.517647 0.776316
42 MHZ 0.517647 0.772152
43 SFG 0.511628 0.814286
44 ADP BEF 0.511628 0.734177
45 50T 0.511628 0.776316
46 ACP 0.511628 0.766234
47 ATP 0.511628 0.786667
48 BEF ADP 0.511628 0.734177
49 ATP MG 0.511364 0.753247
50 G5A 0.511364 0.689655
51 A7D 0.505882 0.869565
52 APC 0.505747 0.75641
53 PRX 0.505747 0.74359
54 AQP 0.505747 0.786667
55 AR6 0.505747 0.786667
56 APR 0.505747 0.786667
57 5FA 0.505747 0.786667
58 ANP 0.505618 0.766234
59 ANP MG 0.505495 0.725
60 7D7 0.5 0.808824
61 ADP PO3 0.5 0.783784
62 SAP 0.5 0.746835
63 RBY 0.5 0.75641
64 AGS 0.5 0.746835
65 Y3J 0.5 0.791045
66 AD9 0.5 0.766234
67 ADV 0.5 0.75641
68 A5A 0.494505 0.674419
69 5X8 0.494253 0.855072
70 SSA 0.48913 0.689655
71 ADP VO4 0.48913 0.753247
72 VO4 ADP 0.48913 0.753247
73 TAT 0.488889 0.75641
74 GAP 0.488889 0.789474
75 ACQ 0.488889 0.766234
76 VMS 0.483871 0.659091
77 52H 0.483871 0.651685
78 54H 0.483871 0.659091
79 5AL 0.483516 0.753247
80 SA8 0.483146 0.810811
81 A5D 0.483146 0.828571
82 A3G 0.481928 0.897059
83 NEC 0.481928 0.865672
84 3AM 0.481481 0.77027
85 NVA LMS 0.479167 0.637363
86 53H 0.478723 0.651685
87 TSB 0.478723 0.686047
88 5CA 0.478723 0.689655
89 MAP 0.478723 0.746835
90 ADP ALF 0.478261 0.725
91 ATF 0.478261 0.75641
92 ALF ADP 0.478261 0.725
93 SAH 0.477778 0.830986
94 SAI 0.477778 0.819444
95 OOB 0.473684 0.753247
96 S7M 0.473118 0.766234
97 SRP 0.473118 0.75641
98 SAM 0.472527 0.766234
99 P5A 0.469388 0.659341
100 DSZ 0.46875 0.670455
101 ADQ 0.46875 0.789474
102 4AD 0.46875 0.746835
103 NSS 0.46875 0.670455
104 LSS 0.46875 0.637363
105 0UM 0.46875 0.8
106 EEM 0.467391 0.766234
107 AAT 0.467391 0.835616
108 AHX 0.463918 0.75
109 00A 0.463918 0.716049
110 DLL 0.463918 0.753247
111 A22 0.463158 0.776316
112 DAL AMP 0.463158 0.753247
113 ADP BMA 0.459184 0.789474
114 LEU LMS 0.459184 0.637363
115 5SV 0.458333 0.707317
116 25A 0.458333 0.763158
117 S8M 0.458333 0.797297
118 8QN 0.458333 0.753247
119 SMM 0.457447 0.7375
120 3AD 0.454545 0.878788
121 KAA 0.454545 0.666667
122 A3S 0.454545 0.882353
123 GSU 0.454545 0.651685
124 A A 0.454545 0.763158
125 A1R 0.453608 0.782051
126 PAJ 0.453608 0.740741
127 AMO 0.453608 0.75641
128 2AM 0.451219 0.783784
129 YLA 0.45045 0.746988
130 BIS 0.45 0.7375
131 TXA 0.45 0.75641
132 PTJ 0.45 0.707317
133 NB8 0.45 0.728395
134 JB6 0.45 0.716049
135 A3P 0.448276 0.76
136 YSA 0.446602 0.651685
137 OAD 0.444444 0.766234
138 A3T 0.444444 0.895522
139 3UK 0.444444 0.74359
140 GEK 0.443299 0.797297
141 AMP DBH 0.442308 0.766234
142 4UV 0.442308 0.746835
143 LAD 0.44 0.740741
144 CC5 0.44 0.863636
145 PR8 0.44 0.731707
146 WAQ 0.44 0.716049
147 7D5 0.439024 0.727273
148 YAP 0.436893 0.725
149 FA5 0.436893 0.734177
150 FYA 0.435644 0.753247
151 1ZZ 0.435644 0.682353
152 ME8 0.435644 0.702381
153 3OD 0.435644 0.766234
154 SXZ 0.435644 0.766234
155 OVE 0.435294 0.753247
156 62X 0.434343 0.759494
157 4UU 0.433962 0.746835
158 XAH 0.432692 0.722892
159 25L 0.431373 0.776316
160 MYR AMP 0.431373 0.682353
161 A6D 0.43 0.734177
162 K15 0.43 0.779221
163 QQX 0.428571 0.705128
164 9SN 0.427184 0.707317
165 ARG AMP 0.425926 0.714286
166 QQY 0.423529 0.714286
167 ACK 0.423529 0.753425
168 SP1 0.423529 0.717949
169 RP1 0.423529 0.717949
170 ATP A A A 0.423077 0.773333
171 YLP 0.422018 0.705882
172 BS5 0.421053 0.67033
173 AFH 0.420561 0.740741
174 7MD 0.420561 0.743902
175 PAP 0.419355 0.773333
176 TYR AMP 0.419048 0.734177
177 D3Y 0.418367 0.857143
178 NAI 0.418182 0.759494
179 4UW 0.418182 0.719512
180 MTP 0.417722 0.791667
181 3L1 0.417722 0.84058
182 3D1 0.417722 0.84058
183 KB1 0.417476 0.8
184 4YB 0.416667 0.637363
185 KH3 0.416667 0.792208
186 2BA 0.41573 0.756757
187 CMP 0.41573 0.767123
188 A2P 0.41573 0.746667
189 AF3 ADP 3PG 0.414414 0.698795
190 2VA 0.413043 0.869565
191 AHZ 0.412844 0.682353
192 2FA 0.4125 0.857143
193 6MD 0.4125 0.880597
194 26A 0.4125 0.855072
195 G3A 0.411215 0.728395
196 7C5 0.411215 0.763158
197 YLC 0.410714 0.743902
198 AP0 0.410714 0.75
199 YLB 0.410714 0.705882
200 48N 0.409091 0.728395
201 5F1 0.407407 0.771429
202 AR6 AR6 0.407407 0.763158
203 G5P 0.407407 0.728395
204 PPS 0.40625 0.690476
205 DND 0.405405 0.75641
206 NXX 0.405405 0.75641
207 7D3 0.404494 0.730769
208 TAD 0.40367 0.719512
209 GTA 0.40367 0.702381
210 IOT 0.403509 0.697674
211 649 0.401786 0.623656
212 WSA 0.401786 0.659091
213 LAQ 0.4 0.682353
214 SO8 0.4 0.857143
215 VRT 0.4 0.833333
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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