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: 210
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 A4D 0.651515 0.84058
7 5CD 0.651515 0.852941
8 MTA 0.628571 0.816901
9 EP4 0.623188 0.819444
10 M2T 0.614286 0.797297
11 DTA 0.614286 0.830986
12 3DH 0.589041 0.816901
13 A 0.573333 0.786667
14 AMP 0.573333 0.786667
15 6RE 0.565789 0.849315
16 SRA 0.565789 0.746835
17 AOC 0.558442 0.816901
18 AMP MG 0.558442 0.789474
19 DSH 0.558442 0.810811
20 5AD 0.552239 0.791045
21 A2D 0.551282 0.766234
22 A3N 0.551282 0.830986
23 ABM 0.551282 0.766234
24 J7C 0.551282 0.835616
25 ADP 0.55 0.766234
26 GJV 0.544304 0.837838
27 S4M 0.544304 0.7625
28 7D7 0.544118 0.760563
29 BA3 0.5375 0.766234
30 A12 0.5375 0.7375
31 MAO 0.5375 0.775
32 AP2 0.5375 0.7375
33 ADX 0.536585 0.694118
34 5AS 0.530864 0.693182
35 B4P 0.530864 0.766234
36 AP5 0.530864 0.766234
37 SFG 0.53012 0.816901
38 AN2 0.52439 0.779221
39 SON 0.52439 0.7375
40 A7D 0.52439 0.794521
41 Y3J 0.521127 0.768116
42 CA0 0.518072 0.746835
43 MHZ 0.518072 0.797468
44 AU1 0.518072 0.792208
45 M33 0.518072 0.75641
46 ADP MG 0.518072 0.779221
47 Z8B 0.5125 0.916667
48 50T 0.511905 0.75641
49 ACP 0.511905 0.746835
50 BEF ADP 0.511905 0.759494
51 5X8 0.511905 0.830986
52 ATP 0.511905 0.766234
53 ADP BEF 0.511905 0.759494
54 PRX 0.505882 0.746835
55 APC 0.505882 0.7375
56 5FA 0.505882 0.766234
57 AR6 0.505882 0.766234
58 AQP 0.505882 0.766234
59 APR 0.505882 0.766234
60 EEM 0.5 0.769231
61 AGS 0.5 0.728395
62 SA8 0.5 0.789474
63 RBY 0.5 0.7375
64 AD9 0.5 0.746835
65 A5D 0.5 0.830986
66 SAP 0.5 0.728395
67 A3G 0.5 0.84507
68 3AM 0.5 0.75
69 ADV 0.5 0.7375
70 ADP PO3 0.5 0.810811
71 ATF 0.494382 0.7375
72 ATP MG 0.494253 0.779221
73 SAI 0.494253 0.797297
74 G5A 0.494253 0.712644
75 SAH 0.494253 0.808219
76 GAP 0.488636 0.792208
77 TAT 0.488636 0.7375
78 ACQ 0.488636 0.746835
79 ANP 0.488636 0.792208
80 SAM 0.488636 0.769231
81 ADQ 0.483871 0.746835
82 AAT 0.483146 0.789474
83 5AL 0.483146 0.75641
84 NEC 0.481481 0.788732
85 ADP ALF 0.477778 0.75
86 ALF ADP 0.477778 0.75
87 A5A 0.477778 0.697674
88 7D5 0.474359 0.708861
89 8QN 0.473118 0.75641
90 GEK 0.473118 0.8
91 3AD 0.472973 0.826087
92 ANP MG 0.472527 0.794872
93 SRP 0.472527 0.759494
94 SMM 0.472527 0.740741
95 VO4 ADP 0.472527 0.779221
96 SSA 0.472527 0.693182
97 S7M 0.472527 0.769231
98 ADP VO4 0.472527 0.779221
99 A3S 0.470588 0.830986
100 2AM 0.468354 0.74026
101 PAJ 0.468085 0.702381
102 VMS 0.467391 0.681818
103 54H 0.467391 0.681818
104 52H 0.467391 0.674157
105 A3P 0.464286 0.763158
106 62X 0.463158 0.740741
107 MAP 0.462366 0.772152
108 DAL AMP 0.462366 0.779221
109 A22 0.462366 0.75641
110 53H 0.462366 0.674157
111 TSB 0.462366 0.689655
112 5CA 0.462366 0.693182
113 A3T 0.45977 0.816901
114 KB1 0.459184 0.779221
115 CC5 0.458333 0.838235
116 ADP BMA 0.458333 0.769231
117 K15 0.458333 0.759494
118 5SV 0.457447 0.710843
119 25A 0.457447 0.766234
120 S8M 0.457447 0.875
121 OOB 0.457447 0.75641
122 QQY 0.45679 0.696203
123 GSU 0.453608 0.693182
124 3D1 0.453333 0.791667
125 3L1 0.453333 0.791667
126 0UM 0.452632 0.779221
127 NSS 0.452632 0.712644
128 A1R 0.452632 0.7625
129 AMO 0.452632 0.759494
130 DSZ 0.452632 0.693182
131 4AD 0.452632 0.772152
132 LSS 0.452632 0.677778
133 7D3 0.452381 0.691358
134 OVE 0.451219 0.7125
135 PAP 0.449438 0.753247
136 BIS 0.44898 0.719512
137 ME8 0.44898 0.705882
138 DLL 0.447917 0.75641
139 NVA LMS 0.447917 0.696629
140 00A 0.447917 0.719512
141 AHX 0.447917 0.753086
142 QQX 0.444444 0.6875
143 3UK 0.443299 0.746835
144 OAD 0.443299 0.746835
145 A6D 0.443299 0.828947
146 LEU LMS 0.443299 0.696629
147 5F1 0.441558 0.774648
148 RP1 0.439024 0.721519
149 SP1 0.439024 0.721519
150 ACK 0.439024 0.733333
151 KAA 0.438776 0.688889
152 PR8 0.438776 0.73494
153 LAD 0.438776 0.743902
154 WAQ 0.438776 0.719512
155 P5A 0.438776 0.681319
156 A A 0.438776 0.789474
157 7C5 0.436893 0.766234
158 PPS 0.434783 0.674419
159 SXZ 0.434343 0.746835
160 JB6 0.434343 0.719512
161 TXA 0.434343 0.7375
162 FYA 0.434343 0.779221
163 PTJ 0.434343 0.710843
164 3OD 0.434343 0.746835
165 NB8 0.434343 0.753086
166 1ZZ 0.434343 0.686047
167 AFH 0.432692 0.702381
168 CMP 0.430233 0.77027
169 2BA 0.430233 0.76
170 A2P 0.430233 0.75
171 25L 0.43 0.75641
172 MYR AMP 0.43 0.705882
173 2FA 0.428571 0.783784
174 26A 0.428571 0.756757
175 KH3 0.428571 0.75
176 4UV 0.427184 0.728395
177 NOC 0.426667 0.782609
178 9SN 0.425743 0.710843
179 V3L 0.423913 0.766234
180 2A5 0.422222 0.703704
181 YAP 0.421569 0.75
182 FA5 0.421569 0.759494
183 ATP A A A 0.421569 0.8
184 4UU 0.419048 0.728395
185 AR6 AR6 0.419048 0.789474
186 NVA 2AD 0.417582 0.783784
187 ATR 0.417582 0.74026
188 XAH 0.417476 0.746988
189 YSA 0.417476 0.693182
190 TYR AMP 0.417476 0.782051
191 D3Y 0.416667 0.808219
192 7D4 0.41573 0.691358
193 MTP 0.415584 0.723684
194 AMP DBH 0.413462 0.769231
195 AHZ 0.411215 0.705882
196 2VA 0.411111 0.794521
197 1DA 0.410256 0.84058
198 6MD 0.410256 0.802817
199 G3A 0.409524 0.731707
200 48N 0.407407 0.731707
201 7MD 0.40566 0.746988
202 G5P 0.40566 0.731707
203 DND 0.40367 0.759494
204 NXX 0.40367 0.759494
205 6V0 0.40367 0.731707
206 GTA 0.401869 0.72619
207 4YB 0.401869 0.677778
208 TAD 0.401869 0.702381
209 101 0.4 0.730769
210 649 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: 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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