Receptor
PDB id Resolution Class Description Source Keywords
6RBS 2.32 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEXE WITH AN ADENINE DERIVATIVE LISTERIA MONOCYTOGENES SEROVAR 1/2A (SATCC BAA-679 / 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
JXT A:302;
 Valid;
 none;
 submit data
280.124 C10 H10 Br N5 C#CCC...
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: JXT; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 JXT 1 1
2 JYT 0.685185 0.79661
3 JXK 0.685185 0.886792
4 JYW 0.660714 0.783333
5 JY2 0.6 0.846154
6 JYE 0.596774 0.854545
7 JXB 0.578125 0.839286
8 JYK 0.539683 0.836364
9 JXN 0.535714 0.862745
10 JYB 0.419355 0.803922
11 PU9 0.418605 0.712121
Similar Ligands (3D)
Ligand no: 1; Ligand: JXT; Similar ligands found: 225
No: Ligand Similarity coefficient
1 AC2 0.9372
2 JXQ 0.9277
3 QUB 0.9252
4 4Z9 0.9247
5 TRP 0.9237
6 JXW 0.9228
7 IOP 0.9216
8 9BF 0.9196
9 3IB 0.9182
10 96R 0.9150
11 CTE 0.9149
12 LTN 0.9149
13 EV3 0.9148
14 HWH 0.9127
15 DTR 0.9125
16 LZB 0.9124
17 KF5 0.9115
18 22T 0.9111
19 JXZ 0.9106
20 DTE 0.9101
21 ARP 0.9071
22 8HG 0.9069
23 EV2 0.9048
24 8Y7 0.9044
25 C0W 0.9029
26 ASE 0.9029
27 5V7 0.9025
28 APS 0.9022
29 XJ2 0.9020
30 NWD 0.9007
31 MFZ 0.9004
32 X04 0.9002
33 7MX 0.9000
34 GZV 0.8993
35 3IL 0.8992
36 VYM 0.8990
37 B5A 0.8988
38 GSY 0.8983
39 4OG 0.8981
40 TSR 0.8977
41 8RK 0.8972
42 ALN 0.8970
43 2GQ 0.8958
44 96Z 0.8958
45 CX4 0.8952
46 X0T 0.8949
47 JHY 0.8943
48 1QP 0.8942
49 B41 0.8938
50 XEN 0.8927
51 FWD 0.8926
52 BIO 0.8925
53 SY4 0.8923
54 52F 0.8923
55 2K8 0.8920
56 PMM 0.8919
57 F5C 0.8915
58 NPL 0.8906
59 HBI 0.8905
60 CG 0.8902
61 H4B 0.8899
62 IOS 0.8893
63 APQ 0.8888
64 ITW 0.8878
65 1Q4 0.8875
66 AMR 0.8872
67 HA6 0.8866
68 22L 0.8864
69 PLP 0.8862
70 EXR 0.8861
71 F52 0.8857
72 67Y 0.8855
73 TSS 0.8853
74 CWD 0.8851
75 NBV 0.8851
76 Q5M 0.8848
77 54X 0.8846
78 9KZ 0.8846
79 ZIP 0.8840
80 P1J 0.8838
81 9F8 0.8837
82 PE2 0.8836
83 EXL 0.8835
84 ETV 0.8830
85 92O 0.8829
86 NAL 0.8822
87 PMP 0.8822
88 C4E 0.8820
89 EY7 0.8819
90 SRO 0.8819
91 D8Q 0.8813
92 BWD 0.8806
93 5WU 0.8806
94 SBK 0.8805
95 YF3 0.8799
96 M3Q 0.8796
97 EYA 0.8795
98 YKG 0.8793
99 5WN 0.8789
100 RVE 0.8788
101 PVQ 0.8785
102 NIP 0.8784
103 D87 0.8783
104 CIY 0.8781
105 PVK 0.8778
106 OUB 0.8778
107 3SU 0.8776
108 CPW 0.8775
109 ZON 0.8775
110 SYE 0.8774
111 B0K 0.8773
112 KWQ 0.8772
113 ML1 0.8772
114 H2B 0.8771
115 JTF 0.8771
116 FXH 0.8771
117 B61 0.8770
118 DAH 0.8770
119 IWD 0.8768
120 QMS 0.8767
121 THM 0.8765
122 96U 0.8763
123 P9T 0.8761
124 5B2 0.8757
125 BGN 0.8755
126 78U 0.8754
127 C09 0.8751
128 2UD 0.8751
129 CGW 0.8750
130 K82 0.8749
131 NFM 0.8749
132 OSB 0.8747
133 KP2 0.8745
134 BHS 0.8744
135 SJK 0.8744
136 MD6 0.8743
137 LP8 0.8736
138 R4E 0.8735
139 DHC 0.8734
140 5ER 0.8732
141 BB4 0.8730
142 NIY 0.8728
143 G6P 0.8728
144 9UL 0.8720
145 PH2 0.8717
146 I2E 0.8715
147 8GK 0.8715
148 M78 0.8712
149 4B0 0.8708
150 M5H 0.8706
151 KOM 0.8702
152 ONZ 0.8702
153 NEO 0.8702
154 KWH 0.8699
155 ZYW 0.8699
156 7AP 0.8697
157 GO8 0.8690
158 0LH 0.8689
159 ML2 0.8686
160 S0G 0.8684
161 PZ8 0.8680
162 GC2 0.8680
163 EYM 0.8680
164 790 0.8680
165 9LI 0.8679
166 ALE 0.8679
167 BG6 0.8672
168 7M2 0.8672
169 YZ9 0.8670
170 CC5 0.8669
171 9GP 0.8667
172 CUH 0.8667
173 A0O 0.8666
174 7M5 0.8666
175 89J 0.8664
176 7PJ 0.8659
177 5F5 0.8657
178 UQ1 0.8657
179 MW5 0.8656
180 PQZ 0.8655
181 HPT 0.8652
182 B56 0.8651
183 MMS 0.8649
184 5OO 0.8648
185 CFA 0.8641
186 EYY 0.8632
187 4BX 0.8628
188 NEU 0.8626
189 3WJ 0.8622
190 982 0.8613
191 Q0K 0.8611
192 N7I 0.8610
193 BY5 0.8609
194 JAK 0.8608
195 3JN 0.8606
196 EYJ 0.8605
197 7L4 0.8603
198 6QT 0.8599
199 0Q2 0.8598
200 OIA 0.8598
201 QBM 0.8595
202 3XH 0.8593
203 JF2 0.8589
204 4NR 0.8585
205 TWB 0.8581
206 AP6 0.8579
207 ELH 0.8576
208 15A 0.8574
209 LWS 0.8569
210 XJE 0.8568
211 M9N 0.8566
212 2LY 0.8558
213 5NN 0.8554
214 CG8 0.8554
215 EVO 0.8553
216 MN QAY 0.8552
217 092 0.8549
218 4AV 0.8549
219 6XC 0.8544
220 C2Y 0.8543
221 7PS 0.8540
222 3VX 0.8538
223 3D3 0.8531
224 BK9 0.8530
225 5F8 0.8518
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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