Receptor
PDB id Resolution Class Description Source Keywords
6RBZ 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
JXK A:302;
 Valid;
 none;
 submit data
271.117 C8 H11 Br N6 c1nc(...
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: JXK; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 JXK 1 1
2 JYT 0.755102 0.894737
3 JYW 0.72549 0.87931
4 JXT 0.685185 0.886792
5 JYE 0.649123 0.824561
6 JXB 0.627119 0.810345
7 JXN 0.62 0.830189
8 JYK 0.586207 0.807018
9 JYB 0.40678 0.709091
10 JXW 0.40678 0.763636
11 JXZ 0.40678 0.733333
12 JY2 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: JXK; Similar ligands found: 317
No: Ligand Similarity coefficient
1 TSR 0.9322
2 EV3 0.9305
3 LZB 0.9299
4 IOP 0.9297
5 9BF 0.9274
6 APS 0.9268
7 IAC 0.9262
8 TSS 0.9260
9 GSY 0.9245
10 AC2 0.9242
11 0LH 0.9241
12 7MX 0.9229
13 52F 0.9227
14 1QP 0.9216
15 SRO 0.9212
16 7FF 0.9207
17 5V7 0.9200
18 ARP 0.9190
19 DTE 0.9173
20 SBK 0.9173
21 BK9 0.9162
22 96R 0.9157
23 F52 0.9153
24 AMR 0.9152
25 RZH 0.9148
26 PQZ 0.9146
27 MFZ 0.9143
28 S7G 0.9137
29 6VD 0.9134
30 TRP 0.9132
31 2K8 0.9131
32 EY7 0.9124
33 5WU 0.9124
34 KF5 0.9118
35 NVU 0.9112
36 ZZZ 0.9099
37 9F8 0.9098
38 NBV 0.9088
39 0W8 0.9088
40 CIY 0.9082
41 IOS 0.9080
42 LTN 0.9078
43 4Z9 0.9076
44 NFM 0.9074
45 DTR 0.9071
46 KWH 0.9070
47 3IL 0.9054
48 F95 0.9053
49 LZ2 0.9046
50 FXH 0.9043
51 EV2 0.9041
52 B41 0.9041
53 PH2 0.9039
54 PRF 0.9039
55 091 0.9036
56 5NS 0.9031
57 NLA 0.9030
58 8RK 0.9028
59 22T 0.9021
60 NAG 0.9017
61 C2Y 0.9017
62 JHY 0.9010
63 6HP 0.9007
64 NPA 0.9006
65 9LI 0.9004
66 GC2 0.9002
67 I2E 0.9002
68 8Y7 0.8999
69 PQ0 0.8993
70 M4E 0.8993
71 GZV 0.8990
72 57O 0.8990
73 M3Q 0.8989
74 92P 0.8989
75 2LY 0.8989
76 X0T 0.8986
77 C9E 0.8985
78 ITW 0.8983
79 F5C 0.8982
80 67Y 0.8978
81 EYY 0.8974
82 DHY 0.8974
83 NPL 0.8962
84 N7I 0.8962
85 HHR 0.8961
86 MQB 0.8961
87 SYE 0.8957
88 8GK 0.8955
89 MD6 0.8954
90 4AV 0.8954
91 5OO 0.8949
92 QMS 0.8943
93 9R5 0.8943
94 NAL 0.8938
95 KWQ 0.8936
96 EYA 0.8933
97 K82 0.8932
98 LOG 0.8929
99 9KZ 0.8929
100 1KP 0.8926
101 92O 0.8925
102 ZON 0.8925
103 HBI 0.8916
104 982 0.8914
105 HWH 0.8914
106 LP8 0.8914
107 VYM 0.8912
108 IBM 0.8911
109 GOE 0.8911
110 ASE 0.8909
111 PVK 0.8907
112 PVQ 0.8904
113 W81 0.8904
114 GXY 0.8902
115 KW8 0.8899
116 MAG 0.8898
117 S0G 0.8894
118 PMP 0.8893
119 CPW 0.8893
120 B61 0.8892
121 N1E 0.8890
122 MPP 0.8889
123 H7Y 0.8889
124 EYM 0.8884
125 OIA 0.8884
126 3IB 0.8881
127 N2I 0.8881
128 B5A 0.8879
129 IQ5 0.8878
130 7AP 0.8878
131 LTM 0.8877
132 CGW 0.8877
133 H4B 0.8877
134 QUB 0.8875
135 3N1 0.8872
136 4AB 0.8871
137 B56 0.8871
138 54X 0.8870
139 CX4 0.8870
140 BIO 0.8869
141 BB4 0.8858
142 KMY 0.8854
143 FER 0.8853
144 BY5 0.8849
145 DHC 0.8848
146 XEN 0.8848
147 2FY 0.8847
148 YKG 0.8845
149 PQK 0.8845
150 B0K 0.8845
151 TXW 0.8844
152 C0W 0.8843
153 H2B 0.8842
154 7PJ 0.8837
155 ZSP 0.8837
156 LDP 0.8837
157 KLK 0.8835
158 HPT 0.8832
159 GT0 0.8830
160 BHS 0.8825
161 OUB 0.8825
162 5WN 0.8825
163 0J5 0.8822
164 NBG 0.8821
165 OW7 0.8821
166 IWD 0.8820
167 E7R 0.8818
168 PLP 0.8812
169 2EC 0.8811
170 BQ2 0.8808
171 L07 0.8807
172 M78 0.8805
173 P9T 0.8804
174 QBM 0.8803
175 CUH 0.8798
176 M5H 0.8797
177 S8G 0.8794
178 22L 0.8794
179 A0O 0.8793
180 CC5 0.8789
181 30G 0.8789
182 G6P 0.8788
183 2UD 0.8786
184 EAE 0.8783
185 UQ1 0.8783
186 CFA 0.8780
187 64E 0.8778
188 ALE 0.8777
189 Y0V 0.8776
190 LRI 0.8774
191 4BX 0.8774
192 RVE 0.8771
193 GO8 0.8770
194 3VX 0.8770
195 2GQ 0.8768
196 PMM 0.8767
197 MS0 0.8764
198 42J 0.8762
199 E35 0.8759
200 9UL 0.8758
201 GJK 0.8758
202 C8O 0.8756
203 AVR 0.8755
204 CG 0.8751
205 APQ 0.8750
206 GO0 0.8748
207 4FE 0.8747
208 790 0.8745
209 3XH 0.8744
210 HHS 0.8742
211 A7H 0.8740
212 KP2 0.8740
213 PXP 0.8739
214 N91 0.8739
215 JAK 0.8737
216 BG6 0.8737
217 89J 0.8736
218 LL1 0.8731
219 E1P 0.8730
220 N8Y 0.8729
221 CR1 0.8727
222 Z25 0.8725
223 RD4 0.8724
224 JF2 0.8723
225 4ME 0.8721
226 LT2 0.8720
227 YZ9 0.8719
228 3XR 0.8717
229 R4E 0.8712
230 EYJ 0.8711
231 KP6 0.8711
232 61M 0.8710
233 3SU 0.8709
234 NQH 0.8709
235 MQG 0.8705
236 SJK 0.8704
237 AJV 0.8704
238 4R1 0.8704
239 RM1 0.8703
240 PLR 0.8700
241 SNG 0.8696
242 CHQ 0.8696
243 68A 0.8696
244 9H2 0.8694
245 VM1 0.8694
246 DAH 0.8692
247 6L6 0.8692
248 6ME 0.8690
249 CSN 0.8690
250 YOF 0.8689
251 4YO 0.8685
252 3VW 0.8683
253 DQU 0.8682
254 MMS 0.8682
255 B62 0.8681
256 GA2 0.8680
257 2JX 0.8680
258 QH3 0.8680
259 44V 0.8679
260 R9Y 0.8677
261 Q5M 0.8673
262 MP5 0.8673
263 327 0.8673
264 DX2 0.8672
265 4B0 0.8669
266 O2A 0.8667
267 PE2 0.8665
268 6DP 0.8664
269 TWB 0.8664
270 HBO 0.8664
271 L1O 0.8662
272 1Q4 0.8661
273 JU2 0.8660
274 JND 0.8659
275 NGA 0.8658
276 3EB 0.8657
277 TL6 0.8656
278 IPD 0.8654
279 L1Q 0.8654
280 KDV 0.8654
281 DEW 0.8653
282 BNX 0.8644
283 ZIP 0.8642
284 3C4 0.8642
285 28N 0.8641
286 C9M 0.8639
287 F06 0.8639
288 6HO 0.8636
289 BDI 0.8635
290 AEH 0.8634
291 CLI 0.8633
292 6N4 0.8627
293 3TV 0.8623
294 XFE 0.8623
295 8WT 0.8623
296 44W 0.8621
297 B2E 0.8618
298 YO5 0.8616
299 NDG 0.8613
300 MIL 0.8611
301 UFO 0.8608
302 XDE 0.8592
303 KYN 0.8591
304 YF3 0.8590
305 9ZE 0.8590
306 S8D 0.8585
307 KYA 0.8581
308 AZY 0.8570
309 ML2 0.8570
310 5WS 0.8567
311 VXX 0.8564
312 WUB 0.8559
313 7L4 0.8544
314 4KL 0.8544
315 5B2 0.8544
316 CG8 0.8534
317 FF2 0.8530
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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