Receptor
PDB id Resolution Class Description Source Keywords
6RGC 2.19 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
CIT A:301;
 Invalid;
 none;
 submit data
192.124 C6 H8 O7 C(C(=...
K3H A:302;
 Valid;
 none;
 submit data
583.557 C24 H29 N11 O7 CN(CC...
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: K3H; Similar ligands found: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 K3H 1 1
2 K38 0.686275 0.957143
3 K3K 0.663462 0.929577
4 K2W 0.657143 0.905405
5 K2H 0.621359 0.957143
6 K3E 0.590909 0.943662
7 MAO 0.540816 0.780488
8 EP4 0.538462 0.875
9 MHZ 0.524752 0.780488
10 SA8 0.524272 0.818182
11 RAB 0.522727 0.871429
12 XYA 0.522727 0.871429
13 ADN 0.522727 0.871429
14 M2T 0.46875 0.826667
15 5N5 0.462366 0.871429
16 A3N 0.460784 0.914286
17 5CD 0.457447 0.805556
18 A4D 0.457447 0.84507
19 MTA 0.44898 0.873239
20 A 0.445545 0.746835
21 AMP 0.445545 0.746835
22 S4M 0.442308 0.790123
23 3DH 0.44 0.821918
24 62X 0.439655 0.768293
25 DTA 0.438776 0.786667
26 AOC 0.436893 0.873239
27 ADP 0.433962 0.75
28 ABM 0.432692 0.772152
29 45A 0.432692 0.772152
30 A2D 0.432692 0.772152
31 ACQ 0.432432 0.731707
32 AN2 0.429907 0.740741
33 GJV 0.428571 0.75
34 6RE 0.427184 0.759494
35 AMP MG 0.427184 0.75641
36 ADX 0.425926 0.681818
37 CA0 0.425926 0.731707
38 M33 0.425926 0.78481
39 BA3 0.424528 0.772152
40 K15 0.423729 0.765432
41 HEJ 0.422018 0.75
42 5X8 0.422018 0.786667
43 ATP 0.422018 0.75
44 KG4 0.422018 0.731707
45 6YZ 0.421053 0.731707
46 B4P 0.420561 0.772152
47 AP5 0.420561 0.772152
48 K2K 0.420168 0.878378
49 J7C 0.419048 0.769231
50 AQP 0.418182 0.75
51 5FA 0.418182 0.75
52 PRX 0.418182 0.753086
53 ZAS 0.417476 0.766234
54 LMS 0.417476 0.662921
55 ADP MG 0.416667 0.746835
56 AT4 0.416667 0.722892
57 ADP BEF 0.416667 0.746835
58 V2G 0.415929 0.717647
59 AGS 0.414414 0.714286
60 APC MG 0.414414 0.728395
61 KY2 0.413793 0.753086
62 SRA 0.413462 0.710843
63 KB1 0.413223 0.7625
64 KY5 0.413223 0.815789
65 A12 0.411215 0.722892
66 AP2 0.411215 0.722892
67 3BH 0.410526 0.861111
68 DSH 0.409524 0.792208
69 HZ2 0.409449 0.820513
70 ACP 0.409091 0.731707
71 50T 0.409091 0.740741
72 S7M 0.408696 0.731707
73 26A 0.408163 0.861111
74 3AM 0.407767 0.734177
75 5AS 0.407407 0.681319
76 SAM 0.40708 0.775
77 KYB 0.40678 0.753086
78 APR 0.405405 0.75
79 AR6 0.405405 0.75
80 APC 0.405405 0.722892
81 5AD 0.404255 0.771429
82 SON 0.40367 0.702381
83 O8M 0.40367 0.864865
84 EEM 0.403509 0.775
85 5AL 0.403509 0.740741
86 8LE 0.403509 0.714286
87 HY8 0.403101 0.820513
88 ADP PO3 0.401786 0.746835
89 ATP MG 0.401786 0.746835
90 AD9 0.401786 0.731707
91 A22 0.401709 0.7625
92 OAD 0.4 0.753086
93 AU1 0.4 0.731707
94 M8M 0.4 0.783133
Similar Ligands (3D)
Ligand no: 1; Ligand: K3H; Similar ligands found: 1
No: Ligand Similarity coefficient
1 ZNB 0.8800
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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