Receptor
PDB id Resolution Class Description Source Keywords
3V8N 2.38 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH 8-BROMO-5'-AMINO-5'-DEOXYADENOSINE, REACTED WIC ITRATE MOLECULE IN N SITE LISTERIA MONOCYTOGENES LIGAND-SCREENING BY CRYSTALLOGRAPHY TWO-DOMAIN KINASE INORPOLYPHOSPHATE/ATP-NAD KINASE 1 TRANSFERASE
Ref.: SCREENING AND IN SITU SYNTHESIS USING CRYSTALS OF A KINASE LEAD TO A POTENT ANTISTAPHYLOCOCCAL COMPOUND STRUCTURE V. 20 1107 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5CI A:302;
Valid;
none;
submit data
519.261 C16 H19 Br N6 O9 c1nc(...
5NB A:301;
Valid;
none;
submit data
345.153 C10 H13 Br N6 O3 c1nc(...
CIT A:303;
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: 5CI; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 5CI 1 1
2 5NB 0.605263 0.905405
3 8BR 0.54023 0.792683
4 Z8B 0.528736 0.802469
5 ZNB 0.518519 0.784091
6 3BH 0.404762 0.815789
Ligand no: 2; Ligand: 5NB; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 5NB 1 1
2 Z8B 0.686567 0.878378
3 8BR 0.676471 0.842105
4 5CI 0.605263 0.905405
5 3BH 0.53125 0.898551
6 N8M 0.486111 0.821918
7 ZNB 0.469388 0.807229
8 A8M 0.45 0.7625
9 5N5 0.449275 0.910448
10 O8M 0.426829 0.8
11 M8M 0.421687 0.705882
12 C8M 0.416667 0.769231
13 M8E 0.41573 0.674157
14 3F5 0.404762 0.789474
15 K3E 0.40404 0.849315
Similar Ligands (3D)
Ligand no: 1; Ligand: 5CI; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: 5NB; Similar ligands found: 224
No: Ligand Similarity coefficient
1 ADN 0.9736
2 AD3 0.9714
3 5CD 0.9634
4 NOS 0.9618
5 4UO 0.9588
6 GMP 0.9579
7 CFE 0.9551
8 1DA 0.9533
9 5AD 0.9528
10 MTH 0.9525
11 MTA 0.9518
12 PRH 0.9488
13 MTP 0.9458
14 5FD 0.9453
15 MDR 0.9451
16 NWW 0.9445
17 6CR 0.9437
18 HPR 0.9431
19 F01 0.9429
20 MTI 0.9425
21 DBM 0.9416
22 TAL 0.9415
23 Y3J 0.9413
24 RFZ 0.9412
25 FTU 0.9407
26 MTM 0.9405
27 9DI 0.9402
28 M2T 0.9398
29 A4D 0.9397
30 3AD 0.9396
31 6MD 0.9395
32 EKH 0.9389
33 RAB 0.9386
34 2FA 0.9386
35 TBN 0.9382
36 PUR 0.9382
37 IMH 0.9377
38 3D1 0.9376
39 UA2 0.9373
40 5ID 0.9372
41 THM 0.9368
42 RPP 0.9363
43 FMB 0.9363
44 XYA 0.9359
45 ARJ 0.9357
46 NOC 0.9357
47 FMC 0.9353
48 A 0.9327
49 5UD 0.9321
50 5F1 0.9314
51 MCF 0.9313
52 CTN 0.9296
53 0DN 0.9291
54 8HG 0.9290
55 FM2 0.9290
56 2FD 0.9260
57 MCY 0.9253
58 AFX 0.9251
59 GNG 0.9238
60 5BT 0.9238
61 URI 0.9235
62 3DH 0.9233
63 NWQ 0.9232
64 MG7 0.9225
65 CL9 0.9222
66 FM1 0.9217
67 26A 0.9210
68 DCF 0.9199
69 5I5 0.9185
70 IMG 0.9172
71 CC5 0.9167
72 A4G 0.9145
73 H7S 0.9127
74 B86 0.9120
75 13A 0.9118
76 5MD 0.9118
77 ZAS 0.9092
78 SCT 0.9088
79 DK4 0.9081
80 CDY 0.9075
81 URD 0.9072
82 MZR 0.9063
83 38B 0.9060
84 DBS 0.9051
85 ID2 0.9046
86 DUR 0.9042
87 7D7 0.9040
88 Z57 0.9037
89 CTD 0.9037
90 HO4 0.9025
91 3DT 0.9022
92 TO1 0.9019
93 GEO 0.9016
94 NNR 0.9014
95 DNB 0.9010
96 I5A 0.9008
97 7CI 0.9002
98 ACE TRP 0.8980
99 5AE 0.8976
100 ZYW 0.8975
101 AHU 0.8969
102 LLT 0.8965
103 UUA 0.8963
104 DCZ 0.8960
105 9UL 0.8959
106 TYU 0.8958
107 H4B 0.8921
108 A3N 0.8915
109 8DA 0.8915
110 3RP 0.8914
111 XYP AHR 0.8913
112 ZYV 0.8911
113 BHS 0.8903
114 TMC 0.8902
115 XTS 0.8885
116 THU 0.8880
117 Q5M 0.8876
118 1Q4 0.8873
119 BVD 0.8865
120 3L1 0.8861
121 QQY 0.8847
122 SGP 0.8844
123 H2B 0.8836
124 A7M 0.8836
125 IXM 0.8835
126 GA2 0.8831
127 XYP XDN 0.8830
128 MEX 0.8828
129 39Z 0.8816
130 QQX 0.8806
131 4AB 0.8804
132 ACK 0.8803
133 BRD 0.8798
134 DKZ 0.8798
135 ZSP 0.8791
136 2TU 0.8790
137 X2M 0.8782
138 092 0.8780
139 3QI 0.8778
140 MPU 0.8771
141 5V7 0.8766
142 XYP XYP 0.8765
143 TRP 0.8765
144 SGV 0.8764
145 HBI 0.8759
146 A4Q 0.8757
147 ZEB 0.8756
148 XIL 0.8751
149 AJ4 0.8749
150 HDU 0.8748
151 AMP 0.8741
152 3WO 0.8739
153 3WN 0.8739
154 IMP 0.8738
155 XDL XYP 0.8736
156 XYP XIF 0.8735
157 XIF XYP 0.8735
158 P2L 0.8735
159 92O 0.8732
160 XYS XYP 0.8731
161 ER6 0.8730
162 AOC 0.8730
163 5JT 0.8724
164 LVY 0.8718
165 22L 0.8715
166 NXB 0.8715
167 0GA 0.8707
168 64I 0.8694
169 0Q2 0.8689
170 89J 0.8687
171 XYS XYS 0.8680
172 BIO 0.8676
173 AOJ 0.8673
174 AUE 0.8672
175 KP2 0.8671
176 C2M 0.8670
177 TMP 0.8670
178 96Z 0.8668
179 AWE 0.8660
180 6ZW 0.8656
181 DHZ 0.8656
182 JAK 0.8651
183 AUG 0.8651
184 A8Q 0.8651
185 OVE 0.8646
186 Q11 0.8646
187 4E5 0.8640
188 EAT 0.8639
189 0OK 0.8635
190 PIR 0.8635
191 ISX 0.8634
192 QME 0.8633
193 EF2 0.8629
194 14Z 0.8624
195 EV2 0.8624
196 BGC GAL 0.8623
197 IMQ 0.8622
198 GN6 0.8621
199 7EH 0.8618
200 6J9 0.8616
201 3AK 0.8613
202 A4N 0.8613
203 54E 0.8601
204 M02 0.8601
205 CTE 0.8600
206 4OG 0.8596
207 SBI 0.8592
208 GW3 0.8591
209 Y70 0.8590
210 6EL 0.8583
211 QUE 0.8581
212 B2X 0.8577
213 JF8 0.8573
214 SA0 0.8569
215 XYP XYS 0.8567
216 NIY 0.8561
217 NWD 0.8560
218 ZIQ 0.8556
219 WCU 0.8549
220 7FZ 0.8546
221 NQ7 0.8536
222 DTR 0.8536
223 3WK 0.8521
224 Q4G 0.8520
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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