Receptor
PDB id Resolution Class Description Source Keywords
6RGA 2.18 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEXE WITH AN INHIBITOR LISTERIA MONOCYTOGENES EGD-E TETRAMERIC NAD KINASE TRANSFERASE
Ref.: FROM SUBSTRATE TO FRAGMENTS TO INHIBITOR ACTIVEIN VIVOAGAINSTSTAPHYLOCOCCUS AUREUS. ACS INFECT DIS. V. 6 422 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K3E A:302;
 Valid;
 none;
 submit data
569.53 C23 H27 N11 O7 c1nc(...
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 (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 6RGD - K2W C24 H29 N11 O7 c1nc(c2c(n....
4 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
5 6RC5 - JYB C9 H9 N5 CCn1c(nc2c....
6 6RBX - JYT C8 H10 Br N5 O c1nc(c2c(n....
7 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
8 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
9 6RBO - JXQ C11 H13 N5 C#CCCCCn1c....
10 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
11 6RR2 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
12 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
13 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 6RG8 - K2K C19 H21 N11 O3 c1nc(c2c(n....
15 6RBV - JYE C8 H9 Br N8 c1nc(c2c(n....
16 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
17 6RGB - K38 C23 H27 N11 O7 c1nc(c2c(n....
18 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
19 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
20 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
21 6RGC - K3H C24 H29 N11 O7 CN(CC#Cc1n....
22 6RBU - JYK C7 H7 Br N8 c1nc(c2c(n....
23 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 6RBY - JYW C9 H12 Br N5 O c1nc(c2c(n....
25 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
26 6RC3 - JXW C8 H10 Cl N5 Cc1nc2c(nc....
27 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
28 6RBP - JYN C9 H12 N8 c1nc(c2c(n....
29 6RC4 - JXZ C8 H11 N5 O Cc1nc2c(nc....
30 6RBS - JXT C10 H10 Br N5 C#CCCCn1c2....
31 6RBR - JXN C7 H8 Br N5 CCn1c2c(c(....
32 6RG9 - K3K C23 H26 N10 O8 c1nc(c2c(n....
33 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
34 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
35 6RGA - K3E C23 H27 N11 O7 c1nc(c2c(n....
36 6RBW - JXB C9 H11 Br N8 c1nc(c2c(n....
37 6RBQ - JYQ C11 H15 N5 O S CC(=O)SCCC....
38 6RBZ - JXK C8 H11 Br N6 c1nc(c2c(n....
39 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
40 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
41 6RC2 - JY2 C11 H13 N5 Cc1nc2c(nc....
42 6RG7 - K2H C19 H21 N11 O3 CN(CC#Cc1[....
43 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
44 6RC6 - JY5 C13 H15 N5 O2 c1nc(c2c(n....
45 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
70% Homology Family (45)
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 6RGD - K2W C24 H29 N11 O7 c1nc(c2c(n....
4 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
5 6RC5 - JYB C9 H9 N5 CCn1c(nc2c....
6 6RBX - JYT C8 H10 Br N5 O c1nc(c2c(n....
7 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
8 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
9 6RBO - JXQ C11 H13 N5 C#CCCCCn1c....
10 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
11 6RR2 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
12 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
13 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 6RG8 - K2K C19 H21 N11 O3 c1nc(c2c(n....
15 6RBV - JYE C8 H9 Br N8 c1nc(c2c(n....
16 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
17 6RGB - K38 C23 H27 N11 O7 c1nc(c2c(n....
18 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
19 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
20 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
21 6RGC - K3H C24 H29 N11 O7 CN(CC#Cc1n....
22 6RBU - JYK C7 H7 Br N8 c1nc(c2c(n....
23 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 6RBY - JYW C9 H12 Br N5 O c1nc(c2c(n....
25 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
26 6RC3 - JXW C8 H10 Cl N5 Cc1nc2c(nc....
27 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
28 6RBP - JYN C9 H12 N8 c1nc(c2c(n....
29 6RC4 - JXZ C8 H11 N5 O Cc1nc2c(nc....
30 6RBS - JXT C10 H10 Br N5 C#CCCCn1c2....
31 6RBR - JXN C7 H8 Br N5 CCn1c2c(c(....
32 6RG9 - K3K C23 H26 N10 O8 c1nc(c2c(n....
33 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
34 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
35 6RGA - K3E C23 H27 N11 O7 c1nc(c2c(n....
36 6RBW - JXB C9 H11 Br N8 c1nc(c2c(n....
37 6RBQ - JYQ C11 H15 N5 O S CC(=O)SCCC....
38 6RBZ - JXK C8 H11 Br N6 c1nc(c2c(n....
39 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
40 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
41 6RC2 - JY2 C11 H13 N5 Cc1nc2c(nc....
42 6RG7 - K2H C19 H21 N11 O3 CN(CC#Cc1[....
43 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
44 6RC6 - JY5 C13 H15 N5 O2 c1nc(c2c(n....
45 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
50% Homology Family (45)
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 6RGD - K2W C24 H29 N11 O7 c1nc(c2c(n....
4 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
5 6RC5 - JYB C9 H9 N5 CCn1c(nc2c....
6 6RBX - JYT C8 H10 Br N5 O c1nc(c2c(n....
7 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
8 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
9 6RBO - JXQ C11 H13 N5 C#CCCCCn1c....
10 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
11 6RR2 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
12 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
13 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 6RG8 - K2K C19 H21 N11 O3 c1nc(c2c(n....
15 6RBV - JYE C8 H9 Br N8 c1nc(c2c(n....
16 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
17 6RGB - K38 C23 H27 N11 O7 c1nc(c2c(n....
18 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
19 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
20 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
21 6RGC - K3H C24 H29 N11 O7 CN(CC#Cc1n....
22 6RBU - JYK C7 H7 Br N8 c1nc(c2c(n....
23 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 6RBY - JYW C9 H12 Br N5 O c1nc(c2c(n....
25 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
26 6RC3 - JXW C8 H10 Cl N5 Cc1nc2c(nc....
27 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
28 6RBP - JYN C9 H12 N8 c1nc(c2c(n....
29 6RC4 - JXZ C8 H11 N5 O Cc1nc2c(nc....
30 6RBS - JXT C10 H10 Br N5 C#CCCCn1c2....
31 6RBR - JXN C7 H8 Br N5 CCn1c2c(c(....
32 6RG9 - K3K C23 H26 N10 O8 c1nc(c2c(n....
33 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
34 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
35 6RGA - K3E C23 H27 N11 O7 c1nc(c2c(n....
36 6RBW - JXB C9 H11 Br N8 c1nc(c2c(n....
37 6RBQ - JYQ C11 H15 N5 O S CC(=O)SCCC....
38 6RBZ - JXK C8 H11 Br N6 c1nc(c2c(n....
39 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
40 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
41 6RC2 - JY2 C11 H13 N5 Cc1nc2c(nc....
42 6RG7 - K2H C19 H21 N11 O3 CN(CC#Cc1[....
43 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
44 6RC6 - JY5 C13 H15 N5 O2 c1nc(c2c(n....
45 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: K3E; Similar ligands found: 168
No: Ligand ECFP6 Tc MDL keys Tc
1 K3E 1 1
2 K3K 0.891304 0.985294
3 K2W 0.62037 0.930556
4 K38 0.616822 0.985294
5 K3H 0.590909 0.943662
6 AOC 0.585106 0.926471
7 5N5 0.539326 0.897059
8 A2D 0.485149 0.815789
9 LMS 0.484848 0.697674
10 A 0.484848 0.789474
11 AMP 0.484848 0.789474
12 SON 0.480769 0.740741
13 AMP MG 0.48 0.8
14 SRA 0.48 0.75
15 CA0 0.47619 0.772152
16 M33 0.47619 0.782051
17 ADX 0.47619 0.717647
18 BA3 0.475728 0.815789
19 KG4 0.471698 0.772152
20 50T 0.471698 0.782051
21 AP5 0.471154 0.815789
22 ADP 0.471154 0.792208
23 B4P 0.471154 0.815789
24 45A 0.470588 0.769231
25 ABM 0.470588 0.769231
26 ADN 0.467391 0.897059
27 RAB 0.467391 0.897059
28 XYA 0.467391 0.897059
29 AT4 0.466667 0.7625
30 AN2 0.466667 0.782051
31 A12 0.461538 0.7625
32 AP2 0.461538 0.7625
33 ACP 0.457944 0.772152
34 H1Q 0.457944 0.779221
35 ATP 0.457944 0.792208
36 HEJ 0.457944 0.792208
37 5AS 0.457143 0.696629
38 APR 0.453704 0.792208
39 AQP 0.453704 0.792208
40 5FA 0.453704 0.792208
41 AR6 0.453704 0.792208
42 PRX 0.453704 0.75
43 ADP MG 0.45283 0.789474
44 ADP BEF 0.45283 0.789474
45 5CD 0.452632 0.828571
46 A4D 0.452632 0.869565
47 V2G 0.45045 0.756098
48 ATP MG 0.449541 0.789474
49 AD9 0.449541 0.772152
50 ADP PO3 0.449541 0.789474
51 AGS 0.449541 0.753086
52 APC MG 0.449541 0.769231
53 M2T 0.44898 0.776316
54 AU1 0.448598 0.772152
55 G5A 0.445455 0.696629
56 OZV 0.443478 0.792208
57 OOB 0.443478 0.782051
58 ANP 0.441441 0.772152
59 ACQ 0.441441 0.772152
60 GAP 0.441441 0.794872
61 APC 0.440367 0.7625
62 EP4 0.438776 0.821918
63 HQG 0.438596 0.782051
64 S4M 0.438095 0.743902
65 8LE 0.4375 0.731707
66 5AL 0.4375 0.759494
67 TXA 0.436975 0.7625
68 RBY 0.436364 0.7625
69 ADV 0.436364 0.7625
70 DLL 0.435897 0.782051
71 3DH 0.435644 0.819444
72 B1U 0.434426 0.659574
73 DTA 0.434343 0.808219
74 A5A 0.433628 0.681818
75 ALF ADP 0.433628 0.731707
76 ATF 0.433628 0.7625
77 BEF ADP 0.432432 0.769231
78 5SV 0.431034 0.714286
79 MTA 0.43 0.819444
80 SRP 0.429825 0.7625
81 6YZ 0.429825 0.772152
82 8LH 0.429825 0.7625
83 TAT 0.428571 0.7625
84 A3N 0.428571 0.941176
85 T99 0.428571 0.7625
86 GSU 0.428571 0.659341
87 WAQ 0.428571 0.722892
88 AMO 0.42735 0.7625
89 PAJ 0.42735 0.746988
90 7MC 0.426357 0.732558
91 FYA 0.425 0.782051
92 PTJ 0.425 0.714286
93 1ZZ 0.425 0.689655
94 7MD 0.424 0.75
95 A22 0.422414 0.805195
96 DAL AMP 0.422414 0.759494
97 8LQ 0.422414 0.740741
98 53H 0.422414 0.659341
99 QA7 0.422414 0.731707
100 MYR AMP 0.421488 0.689655
101 ANP MG 0.421053 0.759494
102 VO4 ADP 0.421053 0.75
103 MAO 0.420561 0.756098
104 OAD 0.420168 0.772152
105 3UK 0.420168 0.794872
106 AMP DBH 0.419355 0.818182
107 DSH 0.419048 0.813333
108 25A 0.418803 0.792208
109 8QN 0.418803 0.759494
110 5X8 0.418182 0.808219
111 SSA 0.417391 0.696629
112 B5V 0.416667 0.78481
113 LAD 0.416667 0.746988
114 4AD 0.415254 0.753086
115 NSS 0.415254 0.677778
116 LSS 0.415254 0.645161
117 ADQ 0.415254 0.818182
118 A1R 0.415254 0.7875
119 A3R 0.415254 0.7875
120 DSZ 0.415254 0.677778
121 8PZ 0.414634 0.696629
122 FA5 0.414634 0.7625
123 VMS 0.413793 0.666667
124 52H 0.413793 0.659341
125 54H 0.413793 0.666667
126 ZAS 0.413462 0.786667
127 3OD 0.413223 0.772152
128 ME8 0.413223 0.709302
129 NVA LMS 0.411765 0.638298
130 AHX 0.411765 0.756098
131 00A 0.411765 0.743902
132 JNT 0.411765 0.794872
133 GJV 0.411215 0.769231
134 NAI 0.410853 0.7875
135 A5D 0.410714 0.808219
136 MAP 0.410256 0.753086
137 5CA 0.410256 0.696629
138 8X1 0.410256 0.673913
139 TSB 0.410256 0.693182
140 6RE 0.409524 0.779221
141 4YB 0.409449 0.681319
142 LEU LMS 0.408333 0.652174
143 9X8 0.408333 0.753086
144 9ZD 0.40678 0.722892
145 QXP 0.40678 0.741176
146 9ZA 0.40678 0.722892
147 9SN 0.406504 0.756098
148 SFG 0.405405 0.77027
149 K2K 0.404959 0.902778
150 KAA 0.404959 0.673913
151 PR8 0.404959 0.738095
152 7C5 0.404762 0.815789
153 5NB 0.40404 0.849315
154 KMQ 0.403226 0.78481
155 B5M 0.403226 0.775
156 48N 0.403101 0.73494
157 KOY 0.403101 0.849315
158 CNA 0.402985 0.78481
159 J7C 0.401869 0.789474
160 NB8 0.401639 0.73494
161 9K8 0.401639 0.673913
162 BIS 0.401639 0.743902
163 JB6 0.401639 0.743902
164 A7D 0.4 0.847222
165 5AD 0.4 0.768116
166 XAH 0.4 0.729412
167 AAT 0.4 0.792208
168 YSA 0.4 0.677778
Similar Ligands (3D)
Ligand no: 1; Ligand: K3E; Similar ligands found: 0
No: Ligand Similarity coefficient
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; 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: 2) in the query (biounit: 5dhu.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; 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: 3) in the query (biounit: 5dhu.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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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