Receptor
PDB id Resolution Class Description Source Keywords
6RG9 2.08 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
K3K A:301;
 Valid;
 none;
 submit data
570.515 C23 H26 N10 O8 c1nc(...
CIT A:302;
 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: K3K; Similar ligands found: 180
No: Ligand ECFP6 Tc MDL keys Tc
1 K3K 1 1
2 K3E 0.891304 0.985294
3 K2W 0.696078 0.916667
4 K38 0.693069 0.970588
5 K3H 0.663462 0.929577
6 AOC 0.597826 0.940298
7 ADN 0.528736 0.910448
8 XYA 0.528736 0.910448
9 RAB 0.528736 0.910448
10 A 0.510417 0.8
11 AMP 0.510417 0.8
12 ADP 0.49505 0.802632
13 A2D 0.494949 0.826667
14 LMS 0.494845 0.705882
15 AN2 0.490196 0.792208
16 SON 0.490196 0.75
17 AMP MG 0.489796 0.810811
18 SRA 0.489796 0.759494
19 CA0 0.485437 0.782051
20 ADX 0.485437 0.72619
21 BA3 0.485149 0.826667
22 ATP 0.480769 0.802632
23 HEJ 0.480769 0.802632
24 KG4 0.480769 0.782051
25 50T 0.480769 0.792208
26 B4P 0.480392 0.826667
27 AP5 0.480392 0.826667
28 ABM 0.48 0.779221
29 45A 0.48 0.779221
30 AQP 0.47619 0.802632
31 5FA 0.47619 0.802632
32 AT4 0.475728 0.772152
33 AGS 0.471698 0.7625
34 M33 0.471154 0.792208
35 AP2 0.470588 0.772152
36 A12 0.470588 0.772152
37 5N5 0.467391 0.882353
38 ACP 0.466667 0.782051
39 H1Q 0.466667 0.789474
40 5AS 0.466019 0.685393
41 ACQ 0.462963 0.782051
42 5CD 0.462366 0.84058
43 A4D 0.462366 0.882353
44 PRX 0.462264 0.759494
45 APR 0.462264 0.802632
46 AR6 0.462264 0.802632
47 APC 0.462264 0.772152
48 ADP BEF 0.461538 0.8
49 ADP MG 0.461538 0.8
50 V2G 0.458716 0.743902
51 M2T 0.458333 0.786667
52 APC MG 0.457944 0.779221
53 AD9 0.457944 0.782051
54 AU1 0.457143 0.782051
55 A22 0.455357 0.815789
56 25A 0.451327 0.802632
57 OOB 0.451327 0.792208
58 OZV 0.451327 0.802632
59 6YZ 0.45045 0.782051
60 TAT 0.449541 0.772152
61 GAP 0.449541 0.782051
62 T99 0.449541 0.772152
63 ANP 0.449541 0.782051
64 EP4 0.447917 0.808219
65 ADQ 0.447368 0.828947
66 HQG 0.446429 0.792208
67 8LE 0.445455 0.740741
68 5AL 0.445455 0.769231
69 3DH 0.444444 0.830986
70 ADP PO3 0.444444 0.8
71 ATP MG 0.444444 0.8
72 ADV 0.444444 0.772152
73 RBY 0.444444 0.772152
74 DLL 0.443478 0.792208
75 DTA 0.443299 0.819444
76 ATF 0.441441 0.772152
77 ALF ADP 0.441441 0.740741
78 G5A 0.440367 0.685393
79 BEF ADP 0.440367 0.779221
80 OAD 0.439655 0.782051
81 5X8 0.439252 0.819444
82 MTA 0.438776 0.830986
83 5SV 0.438596 0.722892
84 SRP 0.4375 0.772152
85 8LH 0.4375 0.772152
86 A3N 0.436893 0.926471
87 GSU 0.435897 0.666667
88 WAQ 0.435897 0.731707
89 PAJ 0.434783 0.756098
90 LSS 0.434783 0.652174
91 AMO 0.434783 0.772152
92 S4M 0.432692 0.731707
93 FYA 0.432203 0.792208
94 TXA 0.432203 0.772152
95 1ZZ 0.432203 0.697674
96 3OD 0.432203 0.782051
97 PTJ 0.432203 0.722892
98 DAL AMP 0.429825 0.769231
99 8LQ 0.429825 0.75
100 QA7 0.429825 0.740741
101 B1U 0.429752 0.666667
102 A5A 0.428571 0.689655
103 VO4 ADP 0.428571 0.759494
104 25L 0.428571 0.815789
105 ANP MG 0.428571 0.769231
106 MYR AMP 0.428571 0.697674
107 MAO 0.428571 0.743902
108 4YB 0.427419 0.688889
109 9X8 0.42735 0.7625
110 3UK 0.42735 0.805195
111 ADP BMA 0.42735 0.828947
112 AMP DBH 0.42623 0.828947
113 8QN 0.426087 0.769231
114 3AM 0.425743 0.786667
115 SSA 0.424779 0.704545
116 B5V 0.423729 0.794872
117 K2K 0.423729 0.888889
118 NSS 0.422414 0.685393
119 4AD 0.422414 0.7625
120 A1R 0.422414 0.775
121 DSZ 0.422414 0.685393
122 A3R 0.422414 0.775
123 ZAS 0.421569 0.773333
124 8PZ 0.421488 0.704545
125 FA5 0.421488 0.772152
126 52H 0.421053 0.666667
127 54H 0.421053 0.674157
128 VMS 0.421053 0.674157
129 ME8 0.420168 0.717647
130 GJV 0.419048 0.75641
131 NVA LMS 0.418803 0.645161
132 JNT 0.418803 0.805195
133 AHX 0.418803 0.765432
134 00A 0.418803 0.753086
135 6RE 0.417476 0.766234
136 MAP 0.417391 0.7625
137 53H 0.417391 0.666667
138 8X1 0.417391 0.663043
139 5CA 0.417391 0.704545
140 TSB 0.417391 0.701149
141 NAI 0.417323 0.797468
142 LEU LMS 0.415254 0.659341
143 3BH 0.414894 0.898551
144 9ZA 0.413793 0.731707
145 9ZD 0.413793 0.731707
146 QXP 0.413793 0.729412
147 DSH 0.413462 0.8
148 9SN 0.413223 0.765432
149 SFG 0.412844 0.780822
150 LAD 0.411765 0.73494
151 PR8 0.411765 0.72619
152 7C5 0.41129 0.826667
153 7MC 0.410853 0.72093
154 B5M 0.409836 0.78481
155 KMQ 0.409836 0.794872
156 J7C 0.409524 0.776316
157 48N 0.409449 0.743902
158 KOY 0.409449 0.861111
159 5AD 0.408602 0.779412
160 NB8 0.408333 0.743902
161 9K8 0.408333 0.681319
162 BIS 0.408333 0.753086
163 7MD 0.408 0.738095
164 A7D 0.407407 0.859155
165 K2H 0.40678 0.887324
166 SA8 0.405405 0.75641
167 A5D 0.405405 0.819444
168 7D7 0.404255 0.8
169 MHZ 0.40367 0.722892
170 4UV 0.403226 0.78481
171 OMR 0.403101 0.709302
172 A3P 0.401869 0.776316
173 SAH 0.401786 0.797297
174 SAI 0.401786 0.786667
175 LAQ 0.401575 0.697674
176 P5A 0.4 0.655914
177 SMM 0.4 0.731707
178 V47 0.4 0.816901
179 KAA 0.4 0.663043
180 S7M 0.4 0.7375
Similar Ligands (3D)
Ligand no: 1; Ligand: K3K; Similar ligands found: 1
No: Ligand Similarity coefficient
1 ZNB 0.9022
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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