Receptor
PDB id Resolution Class Description Source Keywords
6RC2 2.05 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEXE WITH AN ADENINE DERIVATIVE 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
CIT A:301;
 Invalid;
 none;
 submit data
192.124 C6 H8 O7 C(C(=...
JY2 A:302;
 Valid;
 none;
 submit data
215.254 C11 H13 N5 Cc1nc...
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: JY2; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 JY2 1 1
2 JXW 0.62963 0.897959
3 JXZ 0.62963 0.785714
4 JXT 0.6 0.846154
5 PU9 0.452381 0.681818
6 JYB 0.442623 0.875
7 JXK 0.4 0.75
8 JYT 0.4 0.677419
Similar Ligands (3D)
Ligand no: 1; Ligand: JY2; Similar ligands found: 298
No: Ligand Similarity coefficient
1 JYK 0.9797
2 JYW 0.9772
3 JYE 0.9594
4 JXQ 0.9409
5 QUB 0.9367
6 JXB 0.9313
7 DTE 0.9312
8 AC2 0.9309
9 4Z9 0.9286
10 52F 0.9273
11 TRP 0.9262
12 IOP 0.9252
13 HWH 0.9189
14 DTR 0.9182
15 R4E 0.9165
16 B5A 0.9163
17 KF5 0.9151
18 ASE 0.9148
19 1QP 0.9126
20 LTN 0.9123
21 CTE 0.9121
22 ARP 0.9116
23 ITW 0.9114
24 VYM 0.9109
25 92O 0.9107
26 EV2 0.9104
27 NWD 0.9086
28 APS 0.9085
29 NBV 0.9084
30 NLA 0.9081
31 RVE 0.9080
32 B41 0.9076
33 8Y7 0.9075
34 CX4 0.9075
35 9BF 0.9072
36 8HG 0.9068
37 5V7 0.9055
38 Q5M 0.9055
39 EY7 0.9051
40 8RK 0.9051
41 EV3 0.9049
42 6HP 0.9040
43 JHY 0.9032
44 7MX 0.9031
45 22T 0.9027
46 GNR 0.9026
47 MFZ 0.9023
48 SY4 0.9022
49 IAC 0.9019
50 TSR 0.9016
51 PMM 0.9010
52 EXR 0.9008
53 28S 0.9003
54 2GQ 0.9000
55 5WN 0.8999
56 NVU 0.8992
57 X04 0.8991
58 FWD 0.8989
59 EYA 0.8987
60 96Z 0.8981
61 2K8 0.8981
62 9F8 0.8971
63 BIO 0.8963
64 NAL 0.8960
65 SYE 0.8957
66 3SU 0.8956
67 S7G 0.8953
68 F5C 0.8952
69 HBI 0.8941
70 F95 0.8938
71 67Y 0.8937
72 9KZ 0.8936
73 GA2 0.8935
74 XEN 0.8935
75 AMR 0.8932
76 IOS 0.8932
77 PE2 0.8932
78 7AP 0.8929
79 JTF 0.8929
80 H4B 0.8926
81 BB4 0.8922
82 F52 0.8915
83 SRO 0.8911
84 PLP 0.8910
85 SBK 0.8906
86 PMP 0.8901
87 TSS 0.8899
88 ZIP 0.8895
89 CWD 0.8893
90 LI7 0.8889
91 EYM 0.8885
92 B0K 0.8884
93 PVQ 0.8880
94 BWD 0.8876
95 BHS 0.8875
96 D80 0.8873
97 MD6 0.8873
98 NEU 0.8869
99 LRI 0.8869
100 5WU 0.8863
101 X2M 0.8862
102 2JX 0.8861
103 M3Q 0.8861
104 B61 0.8858
105 3L1 0.8858
106 CG 0.8856
107 CPW 0.8856
108 3IB 0.8855
109 D87 0.8855
110 C0W 0.8855
111 M78 0.8855
112 2SX 0.8855
113 KWQ 0.8853
114 1Q4 0.8853
115 AP6 0.8850
116 ETV 0.8847
117 0LH 0.8846
118 ML2 0.8845
119 ML1 0.8845
120 YKG 0.8845
121 DX2 0.8844
122 NEO 0.8844
123 UQ1 0.8844
124 C4E 0.8843
125 C9E 0.8842
126 PVK 0.8842
127 XJ2 0.8841
128 M5H 0.8834
129 IWD 0.8834
130 H35 0.8832
131 2N0 0.8831
132 QMS 0.8831
133 APQ 0.8830
134 5B2 0.8830
135 X0T 0.8828
136 2LW 0.8825
137 8XL 0.8823
138 NPL 0.8821
139 BDI 0.8820
140 CGW 0.8819
141 3AK 0.8819
142 L07 0.8818
143 J38 0.8813
144 ZSP 0.8811
145 MQB 0.8811
146 2UD 0.8808
147 BC3 0.8808
148 G6P 0.8805
149 KWH 0.8799
150 CC5 0.8799
151 RZH 0.8798
152 ZON 0.8798
153 OIA 0.8797
154 KW8 0.8795
155 NAG 0.8795
156 YZ9 0.8793
157 EXG 0.8788
158 CIY 0.8785
159 PH2 0.8782
160 AIQ 0.8781
161 PQZ 0.8779
162 3VX 0.8776
163 78U 0.8776
164 M9N 0.8775
165 GSY 0.8771
166 GC2 0.8769
167 5ER 0.8768
168 NFM 0.8768
169 MS0 0.8762
170 4FE 0.8759
171 TXW 0.8759
172 LLG 0.8754
173 IBM 0.8754
174 OUB 0.8752
175 3JN 0.8752
176 3IL 0.8748
177 OPA 0.8747
178 EAE 0.8744
179 GJK 0.8743
180 EVO 0.8743
181 4AB 0.8743
182 5AD 0.8742
183 9JT 0.8741
184 BGN 0.8740
185 I2E 0.8740
186 54X 0.8735
187 CUH 0.8733
188 CR1 0.8733
189 K82 0.8732
190 ALE 0.8730
191 BG6 0.8729
192 OTA 0.8729
193 ZYW 0.8728
194 DAH 0.8728
195 SU9 0.8728
196 HBO 0.8725
197 57O 0.8720
198 H2B 0.8720
199 9UL 0.8716
200 7PJ 0.8713
201 E7R 0.8711
202 JXN 0.8711
203 9LI 0.8708
204 DHC 0.8705
205 5OO 0.8705
206 S0G 0.8704
207 5F5 0.8703
208 0XR 0.8702
209 HHR 0.8700
210 89J 0.8697
211 B56 0.8690
212 MDR 0.8690
213 3VW 0.8689
214 LFQ 0.8687
215 D8Q 0.8686
216 9GP 0.8683
217 7L4 0.8682
218 FF2 0.8678
219 982 0.8677
220 2P3 0.8677
221 HA6 0.8676
222 Q9P 0.8676
223 B2E 0.8674
224 MW5 0.8671
225 A0O 0.8671
226 L1O 0.8669
227 3D3 0.8667
228 Z25 0.8664
229 FYR 0.8664
230 790 0.8663
231 SJK 0.8661
232 64F 0.8660
233 92P 0.8660
234 FER 0.8659
235 ZIQ 0.8658
236 CXH 0.8657
237 BY5 0.8651
238 5SJ 0.8651
239 TB8 0.8651
240 GO8 0.8649
241 5E5 0.8648
242 AOJ 0.8648
243 DXK 0.8648
244 0J5 0.8647
245 CFA 0.8647
246 34L 0.8645
247 0DF 0.8642
248 ET0 0.8640
249 N7I 0.8640
250 3EB 0.8640
251 IAG 0.8639
252 15A 0.8638
253 NPA 0.8634
254 QH3 0.8633
255 IPD 0.8632
256 363 0.8631
257 MP5 0.8626
258 MMS 0.8626
259 B4L 0.8625
260 LL1 0.8623
261 TWB 0.8623
262 5WS 0.8617
263 6L6 0.8616
264 3N1 0.8612
265 I59 0.8609
266 QIF 0.8609
267 3D1 0.8605
268 C2Y 0.8603
269 GZV 0.8601
270 5GV 0.8601
271 39Z 0.8601
272 4AV 0.8599
273 3M8 0.8596
274 M4E 0.8596
275 761 0.8594
276 ONZ 0.8594
277 3TV 0.8584
278 P4L 0.8582
279 6N4 0.8582
280 D1Y 0.8576
281 1BW 0.8572
282 PLR 0.8571
283 MN QAY 0.8569
284 1FE 0.8566
285 F40 0.8565
286 9FH 0.8565
287 5F1 0.8564
288 PXP 0.8559
289 JWW 0.8558
290 4BX 0.8558
291 2QV 0.8556
292 MQG 0.8554
293 ZEZ 0.8553
294 TR7 0.8550
295 SER DNF 0.8546
296 LOG 0.8545
297 COL 0.8545
298 DNF SER 0.8544
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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