Receptor
PDB id Resolution Class Description Source Keywords
3V8R 2.39 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 H223E MUTANT FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH 5'-AMINO-8-BROMO-5'-DEOXYADEN 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
5NB A:301;
A:302;
Valid;
Valid;
none;
none;
submit data
345.153 C10 H13 Br N6 O3 c1nc(...
CIT A:303;
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 (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: 5NB; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 5NB 1 1
2 Z8B 0.686567 0.878378
3 8BR 0.676471 0.842105
4 5CI 0.605263 0.905405
5 3BH 0.53125 0.898551
6 N8M 0.486111 0.821918
7 ZNB 0.469388 0.807229
8 A8M 0.45 0.7625
9 5N5 0.449275 0.910448
10 O8M 0.426829 0.8
11 M8M 0.421687 0.705882
12 C8M 0.416667 0.769231
13 M8E 0.41573 0.674157
14 3F5 0.404762 0.789474
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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