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Receptor
PDB id Resolution Class Description Source Keywords
2I2F 1.9 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF LMNADK1 LISTERIA MONOCYTOGENES CRYSTAL STRUCTURE OF LMNADK1 BOUND TO A NAD ANALOG TRANSFER
Ref.: NAD KINASES USE SUBSTRATE-ASSISTED CATALYSIS FOR SP RECOGNITION OF NAD. J.BIOL.CHEM. V. 282 33925 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:301;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAD A:274;
Valid;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
PO4 A:273;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
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: NAD; Similar ligands found: 230
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NHD 0.821429 0.972222
3 NAP 0.811966 0.986111
4 NFD 0.791304 0.946667
5 NXX 0.765766 0.972603
6 DND 0.765766 0.972603
7 AMP NAD 0.74359 0.972222
8 ZID 0.737705 0.986111
9 NAQ 0.729508 0.934211
10 NAE 0.721311 0.959459
11 NA0 0.712 0.972603
12 TAP 0.704 0.921053
13 NDE 0.689922 0.972603
14 NAJ 0.683333 0.972222
15 NDC 0.679389 0.934211
16 NDO 0.674603 0.958904
17 N01 0.656 0.972222
18 CNA 0.642276 0.972603
19 NBP 0.621212 0.922078
20 8ID 0.609756 0.922078
21 A2D 0.576923 0.958333
22 ADP 0.575472 0.931507
23 NGD 0.574803 0.922078
24 BA3 0.566038 0.958333
25 M33 0.564815 0.918919
26 ADP PO3 0.563636 0.957747
27 B4P 0.560748 0.958333
28 AP5 0.560748 0.958333
29 AN2 0.555556 0.918919
30 AT4 0.555556 0.894737
31 GAP 0.553571 0.932432
32 OOB 0.551724 0.972222
33 CA0 0.550459 0.932432
34 9JJ 0.546053 0.898734
35 HEJ 0.545455 0.931507
36 ACP 0.545455 0.906667
37 ATP 0.545455 0.931507
38 DQV 0.544 0.972222
39 ADP ALF 0.54386 0.883117
40 ALF ADP 0.54386 0.883117
41 DAL AMP 0.543103 0.945205
42 APR 0.540541 0.931507
43 AQP 0.540541 0.931507
44 AR6 0.540541 0.931507
45 5FA 0.540541 0.931507
46 ADP VO4 0.53913 0.945205
47 VO4 ADP 0.53913 0.945205
48 AD9 0.535714 0.906667
49 SAP 0.535714 0.883117
50 AGS 0.535714 0.883117
51 WAQ 0.533333 0.896104
52 ABM 0.53271 0.905405
53 DLL 0.529412 0.972222
54 00A 0.529412 0.921053
55 ACQ 0.526316 0.906667
56 NJP 0.526316 0.959459
57 ANP 0.526316 0.906667
58 OAD 0.525 0.932432
59 ADX 0.522523 0.839506
60 5AL 0.521739 0.945205
61 A1R 0.521008 0.871795
62 9SN 0.520325 0.909091
63 A 0.518868 0.930556
64 AMP 0.518868 0.930556
65 50T 0.517857 0.893333
66 ATF 0.517241 0.894737
67 1ZZ 0.516393 0.851852
68 3OD 0.516393 0.932432
69 SON 0.513514 0.92
70 PRX 0.513274 0.881579
71 6YZ 0.512821 0.906667
72 SRP 0.512821 0.92
73 9X8 0.512397 0.883117
74 ADP BMA 0.512397 0.932432
75 3UK 0.512397 0.958904
76 MYR AMP 0.512195 0.851852
77 NAJ PZO 0.510949 0.909091
78 NMN 0.509434 0.875
79 A3R 0.508333 0.871795
80 B5V 0.508197 0.945946
81 AMP DBH 0.507937 0.906667
82 A22 0.504202 0.945205
83 ATP A A A 0.504 0.971831
84 B5M 0.504 0.933333
85 FA5 0.504 0.945946
86 8QN 0.5 0.945205
87 NAX 0.496183 0.886076
88 TYR AMP 0.496063 0.933333
89 PR8 0.495935 0.8625
90 AMO 0.495868 0.92
91 ADQ 0.495868 0.932432
92 4AD 0.495868 0.933333
93 PAJ 0.495868 0.873418
94 A12 0.495495 0.894737
95 AP2 0.495495 0.894737
96 AHZ 0.492308 0.851852
97 YAP 0.492063 0.933333
98 FYA 0.491935 0.918919
99 AHX 0.491803 0.884615
100 4UU 0.488372 0.933333
101 5SV 0.487603 0.8375
102 TAT 0.487179 0.894737
103 T99 0.487179 0.894737
104 APC 0.486957 0.894737
105 SRA 0.486239 0.881579
106 6V0 0.484848 0.909091
107 NAI 0.484848 0.921053
108 GTA 0.484615 0.898734
109 A A 0.483871 0.958333
110 LAD 0.483871 0.873418
111 AU1 0.482456 0.906667
112 F2R 0.481752 0.831325
113 OMR 0.481203 0.841463
114 TXE 0.481203 0.921053
115 AF3 ADP 3PG 0.481203 0.873418
116 LAQ 0.480916 0.851852
117 G3A 0.48062 0.909091
118 B5Y 0.480315 0.933333
119 NB8 0.48 0.884615
120 TXA 0.48 0.92
121 BIS 0.48 0.871795
122 ME8 0.48 0.851852
123 PTJ 0.48 0.884615
124 139 0.477941 0.886076
125 LPA AMP 0.477273 0.851852
126 AFH 0.476923 0.873418
127 AR6 AR6 0.476923 0.958333
128 G5P 0.476923 0.909091
129 ARG AMP 0.476923 0.841463
130 25L 0.47619 0.945205
131 NAJ PYZ 0.475524 0.864198
132 25A 0.47541 0.958333
133 9ZA 0.47541 0.896104
134 9ZD 0.47541 0.896104
135 DZD 0.47482 0.897436
136 TXD 0.473684 0.921053
137 4UV 0.472868 0.933333
138 TYM 0.470149 0.945946
139 RBY 0.470085 0.894737
140 ADV 0.470085 0.894737
141 4TA 0.467626 0.864198
142 48N 0.466165 0.884615
143 XAH 0.465116 0.851852
144 4UW 0.462687 0.897436
145 M24 0.461538 0.886076
146 80F 0.460993 0.853659
147 IOT 0.459854 0.821429
148 T5A 0.456522 0.853659
149 EAD 0.455782 0.886076
150 MAP 0.455285 0.883117
151 GA7 0.454545 0.894737
152 BT5 0.453901 0.821429
153 A4P 0.452555 0.833333
154 UP5 0.451852 0.933333
155 PAP 0.445378 0.917808
156 4TC 0.445255 0.909091
157 AP0 0.445255 0.884615
158 YLP 0.444444 0.831325
159 P1H 0.443709 0.864198
160 AOC 0.442478 0.810811
161 Z5A 0.439189 0.833333
162 LMS 0.4375 0.817073
163 2A5 0.436975 0.857143
164 A G 0.43662 0.921053
165 G A A A 0.43662 0.909091
166 COD 0.43662 0.802326
167 ADJ 0.435714 0.841463
168 YLB 0.434783 0.831325
169 YLC 0.434783 0.851852
170 U A G G 0.433566 0.921053
171 ATR 0.433333 0.90411
172 7MD 0.432836 0.851852
173 8X1 0.432 0.764045
174 G5A 0.429752 0.790698
175 PO4 PO4 A A A A PO4 0.429688 0.943662
176 TAD 0.42963 0.873418
177 5AS 0.42735 0.770115
178 BTX 0.426573 0.831325
179 YLA 0.425532 0.831325
180 DSZ 0.425197 0.790698
181 NCN 0.424779 0.805556
182 UPA 0.42446 0.921053
183 8PZ 0.424242 0.811765
184 VMS 0.424 0.8
185 54H 0.424 0.8
186 9K8 0.423077 0.744444
187 N0B 0.422819 0.853659
188 6AD 0.422764 0.85
189 AYB 0.422535 0.821429
190 7D3 0.422414 0.844156
191 YLY 0.421769 0.821429
192 TSB 0.420635 0.809524
193 ODP 0.41958 0.922078
194 AV2 0.419355 0.855263
195 FB0 0.419355 0.775281
196 A5A 0.419355 0.819277
197 NNR 0.419048 0.739726
198 A A A 0.418605 0.918919
199 U A 0.417808 0.946667
200 649 0.417266 0.775281
201 NMN AMP PO4 0.416667 0.933333
202 SSA 0.416 0.790698
203 P5A 0.415385 0.755556
204 LSS 0.414062 0.772727
205 A2R 0.412698 0.918919
206 52H 0.412698 0.790698
207 JB6 0.412214 0.896104
208 5N5 0.411215 0.783784
209 YSA 0.410448 0.811765
210 53H 0.409449 0.790698
211 5CA 0.409449 0.790698
212 ITT 0.408333 0.878378
213 7D4 0.408333 0.844156
214 NA7 0.407692 0.894737
215 LEU LMS 0.407692 0.784091
216 5CD 0.407407 0.794521
217 0WD 0.406897 0.909091
218 A3P 0.40678 0.930556
219 HFD 0.406504 0.883117
220 AVV 0.40625 0.860759
221 RAB 0.40566 0.808219
222 XYA 0.40566 0.808219
223 ADN 0.40566 0.808219
224 FDA 0.405063 0.823529
225 GSU 0.40458 0.790698
226 7MC 0.404255 0.831325
227 NSS 0.403101 0.811765
228 6FA 0.402516 0.853659
229 PPS 0.4 0.817073
230 NVA LMS 0.4 0.784091
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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