Receptor
PDB id Resolution Class Description Source Keywords
4emt 1.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF HUMAN STING BOUND TO C-DI-GMP HOMO SAPIENS ALPHA/BETA FOLD INNATE IMMUNE SENSOR C-DI-GMP C-DI-AMP MPROTEIN
Ref.: STRUCTURE OF STING BOUND TO CYCLIC DI-GMP REVEALS T MECHANISM OF CYCLIC DINUCLEOTIDE RECOGNITION BY THE SYSTEM. NAT.STRUCT.MOL.BIOL. V. 19 722 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:401;
 Valid;
 none;
 Kd = 4.63 uM
690.411 C20 H24 N10 O14 P2 c1nc2...
CA B:401;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6DXL 2.45 Å NON-ENZYME: OTHER LINKED AMIDOBENZIMIDAZOLE STING AGONIST HOMO SAPIENS AGONIST DNA-SENSOR CGAS TBK1 IMMUNE SYSTEM IMMUNE SYSTECOMPLEX
Ref.: DESIGN OF AMIDOBENZIMIDAZOLE STING RECEPTOR AGONIST SYSTEMIC ACTIVITY. NATURE V. 564 439 2018
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4LOI Kd = 0.17 uM 1YC C20 H24 N10 O13 P2 c1nc(c2c(n....
2 6XNP ic50 = 7.8 uM V67 C15 H9 F2 N5 O3 c1cc(nnc1C....
3 6S26 - KT2 C21 H25 N9 O13 P2 c1cn(c2c1c....
4 6DXG ic50 = 14 uM HGJ C23 H24 N6 O3 CCn1c(cc(n....
5 6DXL Kd = 1.6 nM HG4 C34 H38 N12 O4 CCn1c(cc(n....
6 6DNK - 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
7 4EMT Kd = 4.63 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
8 4QXO Kd = 3.12 uM 1YE C17 H14 O4 Cc1ccc2c(c....
9 4QXQ Kd = 1.99 uM 1YE C17 H14 O4 Cc1ccc2c(c....
10 4QXR Kd = 0.99 uM 1YE C17 H14 O4 Cc1ccc2c(c....
11 4LOH Kd = 5.3 uM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4EF4 Kd = 4.42 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
2 5BQX Kd = 1.6 uM 4UR C20 H24 N10 O13 P2 c1nc(c2c(n....
3 6CY7 - 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
4 6CFF - 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
5 4KSY Kd = 3.79 nM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
6 4LOI Kd = 0.17 uM 1YC C20 H24 N10 O13 P2 c1nc(c2c(n....
7 6XNP ic50 = 7.8 uM V67 C15 H9 F2 N5 O3 c1cc(nnc1C....
8 6S26 - KT2 C21 H25 N9 O13 P2 c1cn(c2c1c....
9 6DXG ic50 = 14 uM HGJ C23 H24 N6 O3 CCn1c(cc(n....
10 6DXL Kd = 1.6 nM HG4 C34 H38 N12 O4 CCn1c(cc(n....
11 6DNK - 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
12 4EMT Kd = 4.63 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
13 4QXO Kd = 3.12 uM 1YE C17 H14 O4 Cc1ccc2c(c....
14 4QXQ Kd = 1.99 uM 1YE C17 H14 O4 Cc1ccc2c(c....
15 4QXR Kd = 0.99 uM 1YE C17 H14 O4 Cc1ccc2c(c....
16 4LOH Kd = 5.3 uM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
17 6IYF Kd ~ 6 uM 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
18 6A05 Kd = 12.8 nM 1YD C20 H24 N10 O13 P2 c1nc(c2c(n....
19 6A04 Kd ~ 6 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
20 6A06 Kd = 3.4 nM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
21 4KBY Ka = 5390000 M^-1 C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
22 4LOK Kd = 0.26 uM 1YD C20 H24 N10 O13 P2 c1nc(c2c(n....
23 4LOL Kd = 0.49 uM 1YE C17 H14 O4 Cc1ccc2c(c....
24 6XNN - V67 C15 H9 F2 N5 O3 c1cc(nnc1C....
25 5GRM Kd = 0.12 uM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
50% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4EF4 Kd = 4.42 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
2 5BQX Kd = 1.6 uM 4UR C20 H24 N10 O13 P2 c1nc(c2c(n....
3 6CY7 - 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
4 6CFF - 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
5 4KSY Kd = 3.79 nM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
6 4LOI Kd = 0.17 uM 1YC C20 H24 N10 O13 P2 c1nc(c2c(n....
7 6XNP ic50 = 7.8 uM V67 C15 H9 F2 N5 O3 c1cc(nnc1C....
8 6S26 - KT2 C21 H25 N9 O13 P2 c1cn(c2c1c....
9 6DXG ic50 = 14 uM HGJ C23 H24 N6 O3 CCn1c(cc(n....
10 6DXL Kd = 1.6 nM HG4 C34 H38 N12 O4 CCn1c(cc(n....
11 6DNK - 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
12 4EMT Kd = 4.63 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
13 4QXO Kd = 3.12 uM 1YE C17 H14 O4 Cc1ccc2c(c....
14 4QXQ Kd = 1.99 uM 1YE C17 H14 O4 Cc1ccc2c(c....
15 4QXR Kd = 0.99 uM 1YE C17 H14 O4 Cc1ccc2c(c....
16 4LOH Kd = 5.3 uM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
17 6IYF Kd ~ 6 uM 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
18 6A05 Kd = 12.8 nM 1YD C20 H24 N10 O13 P2 c1nc(c2c(n....
19 6A04 Kd ~ 6 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
20 6A06 Kd = 3.4 nM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
21 4KBY Ka = 5390000 M^-1 C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
22 4LOK Kd = 0.26 uM 1YD C20 H24 N10 O13 P2 c1nc(c2c(n....
23 4LOL Kd = 0.49 uM 1YE C17 H14 O4 Cc1ccc2c(c....
24 6XNN - V67 C15 H9 F2 N5 O3 c1cc(nnc1C....
25 5CFM Kd = 50 nM 4BW C20 H24 N10 O13 P2 c1nc(c2c(n....
26 5CFQ Kd < 1 nM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
27 5CFL Kd = 15 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
28 5CFP - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
29 6UKZ ic50 = 4 nM QBG C28 H25 F O10 S2 COc1cc2c(c....
30 6UKV ic50 = 1.5 nM QB1 C29 H28 O10 S2 COc1cc2cc(....
31 6UKM - QAD C14 H14 O5 S COc1cc2cc(....
32 6UKW - QB7 C29 H27 F O10 S2 COc1cc2cc(....
33 6UKX ic50 = 17 nM QBA C29 H28 O10 S2 COc1cc2cc(....
34 6UKY ic50 = 10 nM QBD C29 H28 O8 S2 COc1cc(c2c....
35 6UL0 ic50 = 16 nM QBJ C29 H26 O9 S2 COc1cc2c(c....
36 6UKU ic50 = 8 nM QAV C29 H28 O8 S2 COc1cc2c(c....
37 5GRM Kd = 0.12 uM 1SY C20 H24 N10 O13 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: C2E; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 0.986111
2 C2E 1 1
3 35G 1 0.986111
4 1YD 0.806818 1
5 4BW 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 KT2 0.669903 1
9 6SW 0.627907 0.944444
10 1YC 0.616162 0.972222
11 6J7 0.58427 0.934211
12 CMP 0.534091 0.902778
13 2BA 0.534091 0.916667
14 GMP 0.53012 0.828947
15 1SY 0.495575 1
16 SGP 0.483871 0.825
17 6SZ 0.483871 0.916667
18 3GP 0.478261 0.92
19 1OR 0.474747 0.741176
20 G 0.468085 0.933333
21 5GP 0.468085 0.933333
22 7CH 0.467391 0.888889
23 6SX 0.462366 0.861111
24 6JR 0.457944 0.944444
25 G2R 0.457143 0.886076
26 GPX 0.451923 0.894737
27 GP3 0.44898 0.947368
28 2GP 0.446809 0.907895
29 GP2 0.444444 0.886076
30 GDP 0.444444 0.921053
31 GNH 0.44 0.909091
32 KB7 0.44 0.780488
33 P2G 0.4375 0.881579
34 G2P 0.436893 0.886076
35 GMV 0.431373 0.897436
36 GTP 0.431373 0.921053
37 ALF 5GP 0.431373 0.841463
38 GDP BEF 0.427184 0.884615
39 G1R 0.427184 0.909091
40 GCP 0.427184 0.897436
41 GTP MG 0.423077 0.907895
42 G3D 0.423077 0.933333
43 GNP 0.423077 0.897436
44 9GM 0.423077 0.897436
45 GSP 0.423077 0.875
46 GDP AF3 0.420561 0.841463
47 G4P 0.415094 0.933333
48 GAV 0.415094 0.886076
49 P1G 0.414141 0.87013
50 KBD 0.412844 0.825
51 Y9Z 0.410714 0.833333
52 GDP ALF 0.407407 0.841463
53 N6R 0.40708 0.831169
54 N6S 0.40708 0.831169
55 G3A 0.403509 0.947368
56 YGP 0.401786 0.876543
57 GPG 0.4 0.935065
58 0O2 0.4 0.933333
59 G5P 0.4 0.947368
Similar Ligands (3D)
Ligand no: 1; Ligand: C2E; Similar ligands found: 1
No: Ligand Similarity coefficient
1 G G 0.9210
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6DXL; Ligand: HG4; 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: 6dxl.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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