Receptor
PDB id Resolution Class Description Source Keywords
2I2B 2.1 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES LISTERIA MONOCYTOGENES CRYSTAL STRUCTURE OF LMNADK1 IN COMPLEX WITH LIGAND ANALOG TRANSFERASE
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
CC5 A:273;
A:274;
Valid;
Valid;
none;
none;
submit data
237.215 C9 H11 N5 O3 c1nc(...
CIT A:301;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
GOL A:401;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(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: CC5; Similar ligands found: 99
No: Ligand ECFP6 Tc MDL keys Tc
1 CC5 1 1
2 5AD 0.568965 0.883333
3 XYA 0.55 0.935484
4 RAB 0.55 0.935484
5 ADN 0.55 0.935484
6 3AD 0.548387 0.95082
7 7D7 0.533333 0.84375
8 Y3J 0.532258 0.854839
9 5N5 0.532258 0.904762
10 A4D 0.52381 0.904762
11 5CD 0.52381 0.919355
12 MTA 0.507463 0.876923
13 RP1 0.5 0.791667
14 EP4 0.5 0.850746
15 SP1 0.5 0.791667
16 DTA 0.492537 0.863636
17 M2T 0.492537 0.826087
18 5F1 0.484848 0.830769
19 3L1 0.476923 0.876923
20 3D1 0.476923 0.876923
21 3DH 0.471429 0.876923
22 2AM 0.471429 0.788732
23 NOC 0.46875 0.84127
24 CMP 0.466667 0.850746
25 2BA 0.466667 0.838235
26 AOC 0.465753 0.90625
27 3AM 0.464789 0.8
28 ZAS 0.458333 0.838235
29 A 0.458333 0.84058
30 AMP 0.458333 0.84058
31 ACK 0.458333 0.782609
32 7D5 0.457143 0.753425
33 OVE 0.452055 0.756757
34 6RE 0.452055 0.828571
35 SRA 0.452055 0.794521
36 AMP MG 0.445946 0.816901
37 A3G 0.445946 0.907692
38 DSH 0.445946 0.84058
39 NEC 0.445946 0.818182
40 QQX 0.444444 0.72973
41 A A A 0.443182 0.830986
42 NA7 0.443182 0.808219
43 5AS 0.441558 0.690476
44 A3N 0.44 0.863636
45 J7C 0.44 0.84058
46 A2D 0.44 0.816901
47 ABM 0.44 0.816901
48 QQY 0.438356 0.739726
49 GJV 0.434211 0.816901
50 S4M 0.434211 0.763158
51 A3P 0.428571 0.814286
52 AP2 0.428571 0.808219
53 A12 0.428571 0.808219
54 BA3 0.428571 0.816901
55 MAO 0.428571 0.776316
56 A2P 0.428571 0.8
57 ARJ 0.426471 0.825397
58 5X8 0.425 0.892308
59 2VA 0.425 0.878788
60 AP5 0.423077 0.816901
61 ADP 0.423077 0.816901
62 B4P 0.423077 0.816901
63 0XU 0.419753 0.848485
64 APC 0.419753 0.808219
65 AN2 0.417722 0.805556
66 A7D 0.417722 0.907692
67 A3S 0.417722 0.921875
68 SON 0.417722 0.808219
69 7D3 0.415584 0.733333
70 M33 0.4125 0.805556
71 ADP MG 0.4125 0.805556
72 AU1 0.4125 0.794521
73 ADX 0.4125 0.734177
74 MHZ 0.4125 0.753247
75 CA0 0.4125 0.794521
76 G5A 0.409639 0.710843
77 D5M 0.407895 0.777778
78 DA 0.407895 0.777778
79 SFG 0.407407 0.876923
80 BEF ADP 0.407407 0.783784
81 50T 0.407407 0.805556
82 ACP 0.407407 0.819444
83 ATP 0.407407 0.816901
84 ADP BEF 0.407407 0.783784
85 A3T 0.407407 0.90625
86 AFX 0.405797 0.73913
87 3AT 0.404762 0.816901
88 A1R 0.404494 0.786667
89 AS 0.402597 0.736842
90 PRX 0.402439 0.794521
91 AR6 0.402439 0.816901
92 2A5 0.402439 0.77027
93 AQP 0.402439 0.816901
94 5FA 0.402439 0.816901
95 APR 0.402439 0.816901
96 54H 0.402299 0.698795
97 VMS 0.402299 0.698795
98 52H 0.402299 0.690476
99 103 0.4 0.736111
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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