Receptor
PDB id Resolution Class Description Source Keywords
2CB3 2.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PEPTIDOGLYCAN RECOGNITION PROTEIN-LE IN COMPLEX WITH TRACHEAL CYTOTOXIN (MONOMERIC D IAMINOPIMELIC ACID-TYPE PEPTIDOGLYCAN) DROSOPHILA MELANOGASTER PGRP TRACHEAL CYTOTOXIN INNATE IMMUNITY IMMUNE SYSTEM
Ref.: STRUCTURAL BASIS FOR PREFERENTIAL RECOGNITION OF DIAMINOPIMELIC ACID-TYPE PEPTIDOGLYCAN BY A SUBSET OF PEPTIDOGLYCAN RECOGNITION PROTEINS J.BIOL.CHEM. V. 281 8286 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1344;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
MLD A:1345;
B:1344;
C:1344;
D:1344;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Kd = 27 nM
921.899 C37 H59 N7 O20 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CB3 2.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PEPTIDOGLYCAN RECOGNITION PROTEIN-LE IN COMPLEX WITH TRACHEAL CYTOTOXIN (MONOMERIC D IAMINOPIMELIC ACID-TYPE PEPTIDOGLYCAN) DROSOPHILA MELANOGASTER PGRP TRACHEAL CYTOTOXIN INNATE IMMUNITY IMMUNE SYSTEM
Ref.: STRUCTURAL BASIS FOR PREFERENTIAL RECOGNITION OF DIAMINOPIMELIC ACID-TYPE PEPTIDOGLYCAN BY A SUBSET OF PEPTIDOGLYCAN RECOGNITION PROTEINS J.BIOL.CHEM. V. 281 8286 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 2CB3 Kd = 27 nM MLD C37 H59 N7 O20 C[C@@H](C(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 2CB3 Kd = 27 nM MLD C37 H59 N7 O20 C[C@@H](C(....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3RT4 Kd = 1.6 nM LP5 C34 H66 N O12 P CCCCCCCCCC....
2 3NG4 - NAG C8 H15 N O6 CC(=O)N[C@....
3 3NW3 Kd = 0.32 uM DGN ALA NDG LAC n/a n/a
4 3O4K Kd = 24 nM LTC C39 H70 N2 O13 CCCCCCCC=C....
5 2CB3 Kd = 27 nM MLD C37 H59 N7 O20 C[C@@H](C(....
6 2APH - AMU ALA GMA LYS DAL DAL NH2 n/a n/a
7 1TWQ - AMU ALA GMA LYS NH2 n/a n/a
8 2EAX Kd = 227 mM ALA FGA LYS DAL DAL AMV NAG n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MLD; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 MLD 1 1
2 NAG AH0 ALA DGL API DAL DAL 0.636986 0.952381
3 ALA NAG AH0 DAL 0.617886 0.885246
4 NAG AH0 0.532787 0.868852
5 ALA FGA LYS DAL DAL AMV NAG 0.506667 0.875
6 MUB ALA NAG ZGL 0.453901 0.885246
7 MUB ALA NAG DGN 0.450704 0.885246
8 AH0 ALA FGA LYS 0.450704 0.920635
9 AMU ALA NAG DGL 0.446809 0.868852
10 AH0 NAG 0.444444 0.868852
11 ALA FGA API DAL DAL MUB 0.426667 0.868852
12 MUB ALA NAG GLN 0.42069 0.868852
13 3QL 0.419355 0.866667
14 AMV ALA FGA LYS DAL DAL 0.417219 0.828125
15 AMU ALA GMA LYS DAL DAL NH2 0.407895 0.84127
16 MUB ALA ZGL ALY DAL NH2 0.405229 0.815385
17 Z4S NAG NAG 0.40458 0.883333
Similar Ligands (3D)
Ligand no: 1; Ligand: MLD; 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 : 2CB3; Ligand: MLD; 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: 2cb3.bio4) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2CB3; Ligand: MLD; 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: 2cb3.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2CB3; Ligand: MLD; 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: 2cb3.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2CB3; Ligand: MLD; 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: 2cb3.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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