Receptor
PDB id Resolution Class Description Source Keywords
6C5K 1.75 Å NON-ENZYME: OTHER S25-23 FAB IN COMPLEX WITH CHLAMYDIACEAE LPS (CRYSTAL FORM 2 MUS MUSCULUS CARBOHYDRATE LIPOPOLYSACCHARIDE ANTIBODY ANTIGEN COMPLEXCHLAMYDIA SUGAR BINDING PROTEIN
Ref.: SUBTLE CHANGES IN THE COMBINING SITE OF THE CHLAMYDIACEAE-SPECIFIC MAB S25-23 INCREASE THE ANTIBODY-CARBOHYDRATE BINDING AFFINITY BY AN ORDER MAGNITUDE. BIOCHEMISTRY V. 58 714 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NO3 B:301;
 Invalid;
 none;
 submit data
62.005 N O3 [N+](...
NAG NAG FUC E:1;
C:1;
 Invalid;
Invalid;
 none;
none;
 submit data
n/a n/a
GP1 Z9M KDO KDO KDO D:1;
F:1;
 Valid;
Valid;
 none;
none;
 Kd = 68.5 nM
1155.78 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C5K 1.75 Å NON-ENZYME: OTHER S25-23 FAB IN COMPLEX WITH CHLAMYDIACEAE LPS (CRYSTAL FORM 2 MUS MUSCULUS CARBOHYDRATE LIPOPOLYSACCHARIDE ANTIBODY ANTIGEN COMPLEXCHLAMYDIA SUGAR BINDING PROTEIN
Ref.: SUBTLE CHANGES IN THE COMBINING SITE OF THE CHLAMYDIACEAE-SPECIFIC MAB S25-23 INCREASE THE ANTIBODY-CARBOHYDRATE BINDING AFFINITY BY AN ORDER MAGNITUDE. BIOCHEMISTRY V. 58 714 2019
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6C5K Kd = 68.5 nM GP1 Z9M KDO KDO KDO n/a n/a
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 67 families.
1 6PXH - DHF C19 H21 N7 O6 c1cc(ccc1C....
2 6C5K Kd = 68.5 nM GP1 Z9M KDO KDO KDO n/a n/a
3 1QKZ - ALA ASN GLY GLY ALA SER GLY GLN VAL LYS n/a n/a
4 2HVK - TBA C16 H36 N CCCC[N+](C....
5 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
6 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
7 6NFV - 1EM C26 H50 O5 CCCCCCCCCC....
8 6NFU - 1EM C26 H50 O5 CCCCCCCCCC....
9 2DWE - TBA C16 H36 N CCCC[N+](C....
10 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 6PXH - DHF C19 H21 N7 O6 c1cc(ccc1C....
4 5DS8 - GLY 5CT GLY ALA n/a n/a
5 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
6 6C5K Kd = 68.5 nM GP1 Z9M KDO KDO KDO n/a n/a
7 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
8 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
9 2HVK - TBA C16 H36 N CCCC[N+](C....
10 5DUB - GLY 5GG GLY ALA n/a n/a
11 5MES Kd = 0.34 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
12 6FS0 Kd = 0.00017 uM E4W C35 H34 Cl N5 O3 S2 Cc1c-2c(nn....
13 5BJZ - GLC GLC n/a n/a
14 3PGF - GLC GLC n/a n/a
15 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
16 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
18 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
19 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
20 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
21 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
22 6NFV - 1EM C26 H50 O5 CCCCCCCCCC....
23 6NFU - 1EM C26 H50 O5 CCCCCCCCCC....
24 2DWE - TBA C16 H36 N CCCC[N+](C....
25 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GP1 Z9M KDO KDO KDO; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 GP1 Z9M KDO KDO KDO 1 1
2 GP1 GP4 KDO KDO KDO 0.900901 1
3 KDA KDO KDO 0.521008 0.683333
4 GN1 GN4 KDO KDO 0.457516 0.833333
5 KDA KDO 0.444444 0.689655
6 GP1 Z9M 0.443478 0.928571
7 KDO KDO KDO 0.416667 0.714286
Similar Ligands (3D)
Ligand no: 1; Ligand: GP1 Z9M KDO KDO KDO; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C5K; Ligand: GP1 Z9M KDO KDO KDO; 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: 6c5k.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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