Receptor
PDB id Resolution Class Description Source Keywords
6C9R 2.1 Å EC: 2.7.1.20 MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE BOUND TO (2R,3S, (HYDROXYMETHYL)-5-(6-(THIOPHEN-3-YL)-9H-PURIN-9-YL)TETRAHYD4 -DIOL MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE ANALOG COMPLEX INHIBITOR STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE TB STRUCTURAL GENOMICS CONSORTBSGC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DRUG DESIGN OF 6-SUBSTITUTED ADENO ANALOGUES AS POTENT INHIBITORS OF MYCOBACTERIUM TUB ADENOSINE KINASE. J.MED.CHEM. V. 62 4483 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:403;
B:403;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
ERJ A:401;
A:402;
B:402;
B:401;
 Valid;
Valid;
Valid;
Valid;
 none;
Atoms found LESS than expected: % Diff = 0.391;
Atoms found LESS than expected: % Diff = 0.391;
none;
 submit data
334.35 C14 H14 N4 O4 S c1csc...
GOL B:404;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C9V 1.7 Å EC: 2.7.1.20 MYCOBACTERIUM TUBERCULOSIS ADENOSINE KINASE BOUND TO (2R,3S, (HYDROXYMETHYL)-5-(6-(4-PHENYLPIPERAZIN-1-YL)-9H-PURIN-9-YLT ETRAHYDROFURAN-3,4-DIOL MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE ANALOG COMPLEX INHIBITOR STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE TB STRUCTURAL GENOMICS CONSORTBSGC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DRUG DESIGN OF 6-SUBSTITUTED ADENO ANALOGUES AS POTENT INHIBITORS OF MYCOBACTERIUM TUB ADENOSINE KINASE. J.MED.CHEM. V. 62 4483 2019
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PVV ic50 = 0.33 uM HO4 C13 H14 N4 O4 C#Cc1cn(c2....
2 6C9V Ki = 120.2 nM ERS C20 H24 N6 O4 c1ccc(cc1)....
3 4O1G - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
4 2PKK - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
5 6C9S - ERP C24 H20 N4 O4 c1ccc(cc1)....
6 2PKM - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6C9Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
8 6C67 - 5ID C11 H13 I N4 O4 c1c(c2c(nc....
9 6C9N - SGV C12 H15 N5 O5 c1c(c2c(nc....
10 6C9R - ERJ C14 H14 N4 O4 S c1cscc1c2c....
11 6C9P - MTP C11 H14 N4 O4 S CSc1c2c(nc....
12 2PKN - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
13 3B1P - NOS C10 H12 N4 O5 c1nc2c(n1[....
14 3B1Q - NOS C10 H12 N4 O5 c1nc2c(n1[....
15 3B1R - AMP MG n/a n/a
16 3B1N - MZR C9 H13 N3 O6 c1nc(c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ERJ; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 ERJ 1 1
2 RAB 0.536232 0.920635
3 XYA 0.536232 0.920635
4 ADN 0.536232 0.920635
5 26A 0.506849 0.878788
6 MTP 0.493151 0.893939
7 6MD 0.486486 0.90625
8 K2R 0.479167 0.746667
9 N6P 0.478723 0.8
10 1DA 0.466667 0.920635
11 5N5 0.44 0.890625
12 A4D 0.434211 0.920635
13 5CD 0.434211 0.846154
14 ERS 0.431818 0.84058
15 M2T 0.43038 0.788732
16 ERP 0.426966 0.920635
17 MTA 0.425 0.835821
18 AMP 0.421687 0.777778
19 A 0.421687 0.777778
20 EP4 0.417722 0.785714
21 DTA 0.4125 0.823529
22 2FA 0.410256 0.852941
23 IMO 0.406977 0.788732
24 ZAS 0.404762 0.774648
25 AMP MG 0.4 0.788732
26 6CR 0.4 0.84058
27 SRA 0.4 0.76
Similar Ligands (3D)
Ligand no: 1; Ligand: ERJ; Similar ligands found: 36
No: Ligand Similarity coefficient
1 123 0.9165
2 1KX 0.9128
3 802 0.9071
4 23M 0.8988
5 FL8 0.8966
6 HMX 0.8937
7 BMZ 0.8880
8 122 0.8880
9 6QT 0.8876
10 120 0.8866
11 CR4 0.8854
12 7DE 0.8805
13 NOS 0.8791
14 15Q 0.8750
15 801 0.8717
16 EUN 0.8707
17 GMP 0.8693
18 47X 0.8689
19 AD3 0.8676
20 6JM 0.8670
21 5ID 0.8658
22 MI2 0.8657
23 OUA 0.8650
24 124 0.8639
25 DQH 0.8637
26 LU2 0.8625
27 5AD 0.8624
28 40N 0.8616
29 JRE 0.8604
30 M5A 0.8601
31 D4O 0.8594
32 GBJ 0.8581
33 22M 0.8574
34 MG7 0.8574
35 521 0.8563
36 Q19 0.8544
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C9V; Ligand: ERS; Similar sites found with APoc: 18
This union binding pocket(no: 1) in the query (biounit: 6c9v.bio1) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 2VAR AMP 6.70927
2 2VAR AMP 6.70927
3 2VAR AMP 6.70927
4 2VAR ANP 6.70927
5 2VAR ANP 6.70927
6 2VAR ANP 6.70927
7 6VWO ADP 8.33333
8 6ILS ATP 8.6262
9 6ILS ATP 8.6262
10 2HW1 FRU 8.72483
11 6A8A ATP 32.4074
12 6A8A ATP 32.4074
13 1V1A ADP 36.8932
14 4XDA ADP 39.1586
15 4XDA ADP 39.1586
16 2C49 ANP 43.0464
17 2C49 ADN 43.0464
18 2C49 ANP 43.0464
Pocket No.: 2; Query (leader) PDB : 6C9V; Ligand: ERS; Similar sites found with APoc: 18
This union binding pocket(no: 2) in the query (biounit: 6c9v.bio1) has 70 residues
No: Leader PDB Ligand Sequence Similarity
1 2VAR AMP 6.70927
2 2VAR AMP 6.70927
3 2VAR AMP 6.70927
4 2VAR ANP 6.70927
5 2VAR ANP 6.70927
6 2VAR ANP 6.70927
7 6VWO ADP 8.33333
8 6ILS ATP 8.6262
9 6ILS ATP 8.6262
10 2HW1 FRU 8.72483
11 6A8A ATP 32.4074
12 6A8A ATP 32.4074
13 1V1A ADP 36.8932
14 4XDA ADP 39.1586
15 4XDA ADP 39.1586
16 2C49 ANP 43.0464
17 2C49 ADN 43.0464
18 2C49 ANP 43.0464
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