Receptor
PDB id Resolution Class Description Source Keywords
6RBY 2.31 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
JYW A:302;
 Valid;
 none;
 submit data
286.128 C9 H12 Br N5 O 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: JYW; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 JYW 1 1
2 JYT 0.833333 0.949153
3 JXK 0.72549 0.87931
4 JXB 0.661017 0.75
5 JXT 0.660714 0.783333
6 JYE 0.627119 0.734375
7 JYK 0.566667 0.71875
8 JXN 0.566038 0.733333
9 JXZ 0.440678 0.790323
Similar Ligands (3D)
Ligand no: 1; Ligand: JYW; Similar ligands found: 159
No: Ligand Similarity coefficient
1 JY2 0.9772
2 JXW 0.9413
3 TRP 0.9370
4 JXQ 0.9323
5 DTR 0.9306
6 EV3 0.9277
7 96Z 0.9276
8 DTE 0.9252
9 4Z9 0.9244
10 B5A 0.9229
11 9F8 0.9203
12 LTN 0.9162
13 CTE 0.9159
14 IAC 0.9148
15 F95 0.9132
16 7MX 0.9130
17 8RK 0.9126
18 IOP 0.9123
19 AC2 0.9111
20 NWD 0.9109
21 GNR 0.9108
22 3IB 0.9098
23 F52 0.9077
24 8XL 0.9076
25 3IL 0.9070
26 ARP 0.9069
27 NLA 0.9065
28 TR7 0.9062
29 M3Q 0.9062
30 9BF 0.9061
31 HWH 0.9060
32 JHY 0.9058
33 ASE 0.9055
34 EY7 0.9055
35 APQ 0.9046
36 FWD 0.9044
37 2N0 0.9034
38 ITW 0.9033
39 CX4 0.9029
40 FT6 0.9018
41 67Y 0.9007
42 RVE 0.9006
43 EXR 0.9000
44 EYA 0.8998
45 8Y7 0.8993
46 7FF 0.8988
47 TSR 0.8988
48 4OG 0.8987
49 VYM 0.8978
50 ZON 0.8975
51 SY4 0.8971
52 M1D 0.8971
53 GSY 0.8966
54 EYY 0.8963
55 SBK 0.8961
56 APS 0.8952
57 IOS 0.8951
58 NVU 0.8949
59 F5C 0.8947
60 I2E 0.8946
61 HBI 0.8935
62 Q5M 0.8934
63 PQZ 0.8927
64 8HG 0.8924
65 0LH 0.8922
66 4AB 0.8922
67 CWD 0.8921
68 BWD 0.8920
69 5WU 0.8913
70 QMS 0.8912
71 MQB 0.8909
72 SRO 0.8907
73 G6P 0.8898
74 R4E 0.8887
75 BB4 0.8879
76 GTV 0.8875
77 CG 0.8873
78 P9T 0.8863
79 XEN 0.8862
80 DAH 0.8861
81 EYM 0.8861
82 YKG 0.8855
83 KWH 0.8850
84 QBM 0.8849
85 IWD 0.8844
86 BG6 0.8844
87 X0T 0.8840
88 TSS 0.8839
89 2SX 0.8835
90 ML2 0.8830
91 KWQ 0.8827
92 PE2 0.8819
93 FXH 0.8816
94 5HG 0.8813
95 7PS 0.8813
96 NBB 0.8812
97 ALN 0.8805
98 4R1 0.8805
99 LRI 0.8802
100 AIQ 0.8799
101 3SU 0.8796
102 5WN 0.8792
103 5F1 0.8786
104 ML1 0.8778
105 DEW 0.8776
106 EVO 0.8771
107 S3C 0.8767
108 K82 0.8767
109 NIY 0.8753
110 IBM 0.8752
111 E7R 0.8748
112 A0O 0.8743
113 2UD 0.8736
114 NAL 0.8736
115 39Z 0.8732
116 64F 0.8728
117 OIA 0.8728
118 QH3 0.8725
119 790 0.8721
120 ALE 0.8719
121 3JL 0.8716
122 GC2 0.8716
123 57O 0.8712
124 AVR 0.8709
125 E35 0.8709
126 3G3 0.8706
127 LLG 0.8703
128 CDY 0.8700
129 GOE 0.8697
130 L21 0.8677
131 6NJ 0.8672
132 5ER 0.8669
133 FIP 0.8669
134 EYJ 0.8664
135 3JM 0.8661
136 S8D 0.8659
137 IPL 0.8659
138 CL9 0.8656
139 EGR 0.8656
140 3EB 0.8655
141 6N4 0.8646
142 GXG 0.8619
143 GO1 0.8617
144 GZV 0.8609
145 9UL 0.8601
146 NPA 0.8599
147 KW8 0.8599
148 7CT 0.8599
149 61M 0.8581
150 3AD 0.8580
151 FSU 0.8572
152 L12 0.8569
153 I59 0.8567
154 QTG 0.8567
155 H7Y 0.8562
156 BQ2 0.8560
157 9PP 0.8550
158 CRZ 0.8540
159 6XC 0.8532
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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