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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: 222
No: Ligand ECFP6 Tc MDL keys Tc
1 ZAS 1 1
2 ADN 0.68254 0.84058
3 RAB 0.68254 0.84058
4 XYA 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 LMS 0.573333 0.714286
14 A 0.573333 0.786667
15 AMP 0.573333 0.786667
16 SRA 0.565789 0.746835
17 6RE 0.565789 0.849315
18 AOC 0.558442 0.816901
19 DSH 0.558442 0.810811
20 5AD 0.552239 0.791045
21 ABM 0.551282 0.766234
22 J7C 0.551282 0.835616
23 A3N 0.551282 0.830986
24 A2D 0.551282 0.766234
25 ADP 0.55 0.766234
26 S4M 0.544304 0.7625
27 GJV 0.544304 0.837838
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 B4P 0.530864 0.766234
35 5AS 0.530864 0.693182
36 AP5 0.530864 0.766234
37 SFG 0.53012 0.816901
38 SON 0.52439 0.7375
39 AT4 0.52439 0.7375
40 A7D 0.52439 0.794521
41 AN2 0.52439 0.779221
42 Y3J 0.521127 0.768116
43 MHZ 0.518072 0.797468
44 AU1 0.518072 0.792208
45 M33 0.518072 0.75641
46 CA0 0.518072 0.746835
47 Z8B 0.5125 0.916667
48 ATP 0.511905 0.766234
49 5X8 0.511905 0.830986
50 HEJ 0.511905 0.766234
51 ACP 0.511905 0.746835
52 50T 0.511905 0.75641
53 APC 0.505882 0.7375
54 APR 0.505882 0.766234
55 PRX 0.505882 0.746835
56 5FA 0.505882 0.766234
57 AQP 0.505882 0.766234
58 AR6 0.505882 0.766234
59 RBY 0.5 0.7375
60 ADV 0.5 0.7375
61 3AM 0.5 0.75
62 AGS 0.5 0.728395
63 SAP 0.5 0.728395
64 EEM 0.5 0.769231
65 A3G 0.5 0.84507
66 ADP PO3 0.5 0.810811
67 AD9 0.5 0.746835
68 A5D 0.5 0.830986
69 SA8 0.5 0.789474
70 ATF 0.494382 0.7375
71 G5A 0.494253 0.712644
72 SAI 0.494253 0.797297
73 SAH 0.494253 0.808219
74 T99 0.488636 0.7375
75 ANP 0.488636 0.792208
76 SAM 0.488636 0.769231
77 TAT 0.488636 0.7375
78 GAP 0.488636 0.792208
79 ACQ 0.488636 0.746835
80 ADQ 0.483871 0.746835
81 AAT 0.483146 0.789474
82 5AL 0.483146 0.75641
83 NEC 0.481481 0.788732
84 A5A 0.477778 0.697674
85 ALF ADP 0.477778 0.75
86 ADP ALF 0.477778 0.75
87 7D5 0.474359 0.708861
88 GEK 0.473118 0.8
89 8QN 0.473118 0.75641
90 3AD 0.472973 0.826087
91 SSA 0.472527 0.693182
92 SMM 0.472527 0.740741
93 VO4 ADP 0.472527 0.779221
94 6YZ 0.472527 0.746835
95 ADP VO4 0.472527 0.779221
96 S7M 0.472527 0.769231
97 SRP 0.472527 0.759494
98 A3S 0.470588 0.830986
99 2AM 0.468354 0.74026
100 PAJ 0.468085 0.702381
101 52H 0.467391 0.674157
102 VMS 0.467391 0.681818
103 54H 0.467391 0.681818
104 A3P 0.464286 0.763158
105 62X 0.463158 0.740741
106 DAL AMP 0.462366 0.779221
107 53H 0.462366 0.674157
108 8X1 0.462366 0.688889
109 TSB 0.462366 0.689655
110 A22 0.462366 0.75641
111 MAP 0.462366 0.772152
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 K15 0.458333 0.759494
117 ADP BMA 0.458333 0.769231
118 9ZD 0.457447 0.740741
119 9ZA 0.457447 0.740741
120 25A 0.457447 0.766234
121 S8M 0.457447 0.875
122 5SV 0.457447 0.710843
123 OOB 0.457447 0.75641
124 QQY 0.45679 0.696203
125 B5V 0.453608 0.7375
126 GSU 0.453608 0.693182
127 3D1 0.453333 0.791667
128 3L1 0.453333 0.791667
129 LSS 0.452632 0.677778
130 DSZ 0.452632 0.693182
131 NSS 0.452632 0.712644
132 4AD 0.452632 0.772152
133 AMO 0.452632 0.759494
134 A3R 0.452632 0.7625
135 A1R 0.452632 0.7625
136 0UM 0.452632 0.779221
137 7D3 0.452381 0.691358
138 OVE 0.451219 0.7125
139 PAP 0.449438 0.753247
140 BIS 0.44898 0.719512
141 ME8 0.44898 0.705882
142 9K8 0.44898 0.634409
143 AHX 0.447917 0.753086
144 NVA LMS 0.447917 0.688889
145 DLL 0.447917 0.75641
146 00A 0.447917 0.719512
147 QQX 0.444444 0.6875
148 3UK 0.443299 0.746835
149 9X8 0.443299 0.728395
150 OAD 0.443299 0.746835
151 LEU LMS 0.443299 0.688889
152 A6D 0.443299 0.828947
153 5F1 0.441558 0.774648
154 SP1 0.439024 0.721519
155 RP1 0.439024 0.721519
156 ACK 0.439024 0.733333
157 P5A 0.438776 0.681319
158 WAQ 0.438776 0.719512
159 LAD 0.438776 0.743902
160 KAA 0.438776 0.688889
161 PR8 0.438776 0.73494
162 A A 0.438776 0.789474
163 7C5 0.436893 0.766234
164 B5M 0.435644 0.728395
165 PPS 0.434783 0.674419
166 1ZZ 0.434343 0.686047
167 TXA 0.434343 0.7375
168 JB6 0.434343 0.719512
169 3OD 0.434343 0.746835
170 PTJ 0.434343 0.710843
171 NB8 0.434343 0.753086
172 SXZ 0.434343 0.746835
173 FYA 0.434343 0.779221
174 AFH 0.432692 0.702381
175 A2P 0.430233 0.75
176 CMP 0.430233 0.77027
177 2BA 0.430233 0.76
178 25L 0.43 0.75641
179 MYR AMP 0.43 0.705882
180 KH3 0.428571 0.75
181 2FA 0.428571 0.783784
182 26A 0.428571 0.756757
183 4UV 0.427184 0.728395
184 NOC 0.426667 0.782609
185 9SN 0.425743 0.710843
186 V3L 0.423913 0.766234
187 2A5 0.422222 0.703704
188 FA5 0.421569 0.759494
189 B5Y 0.421569 0.728395
190 8PZ 0.421569 0.693182
191 ATP A A A 0.421569 0.8
192 YAP 0.421569 0.75
193 AR6 AR6 0.419048 0.789474
194 4UU 0.419048 0.728395
195 ARG AMP 0.419048 0.759036
196 ATR 0.417582 0.74026
197 YSA 0.417476 0.693182
198 XAH 0.417476 0.746988
199 D3Y 0.416667 0.808219
200 7D4 0.41573 0.691358
201 MTP 0.415584 0.723684
202 AMP DBH 0.413462 0.769231
203 TYR AMP 0.413462 0.772152
204 AHZ 0.411215 0.705882
205 2VA 0.411111 0.794521
206 6MD 0.410256 0.802817
207 1DA 0.410256 0.84058
208 G3A 0.409524 0.731707
209 48N 0.407407 0.731707
210 G5P 0.40566 0.731707
211 GA7 0.40566 0.7375
212 7MD 0.40566 0.746988
213 NXX 0.40367 0.759494
214 DND 0.40367 0.759494
215 6V0 0.40367 0.731707
216 NVA 2AD 0.402174 0.8
217 GTA 0.401869 0.72619
218 TAD 0.401869 0.702381
219 4YB 0.401869 0.677778
220 DQV 0.401869 0.75641
221 649 0.4 0.663043
222 101 0.4 0.730769
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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