Receptor
PDB id Resolution Class Description Source Keywords
2VGK 2.25 Å EC: 3.4.16.4 CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN ACTINOMADURA SP. CELL WALL BIOGENESIS/DEGRADATION ANTIBIOTIC RESISTANCE PEPTIDOGLYCAN SYNTHESIS PROTEASE SECRETED HYDROLASE CELL SHAPE CARBOXYPEPTIDASE PENICILLIN-BINDING ACTINOMADURA PEPTIDOGLYCAN TRANSPEPTIDASE
Ref.: CRYSTAL STRUCTURES OF COMPLEXES OF BACTERIAL DD-PEPTIDASES WITH PEPTIDOGLYCAN-MIMETIC LIGANDS: THE SUBSTRATE SPECIFICITY PUZZLE. J.MOL.BIOL. V. 381 383 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:610;
A:611;
D:610;
D:611;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
REZ A:500;
B:500;
C:500;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
246.26 C10 H18 N2 O5 C[C@H...
SO4 A:600;
A:601;
A:602;
A:603;
A:604;
B:600;
B:601;
B:602;
B:603;
B:604;
C:600;
C:601;
C:602;
C:603;
C:604;
D:600;
D:601;
D:602;
D:603;
D:604;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VGK 2.25 Å EC: 3.4.16.4 CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN ACTINOMADURA SP. CELL WALL BIOGENESIS/DEGRADATION ANTIBIOTIC RESISTANCE PEPTIDOGLYCAN SYNTHESIS PROTEASE SECRETED HYDROLASE CELL SHAPE CARBOXYPEPTIDASE PENICILLIN-BINDING ACTINOMADURA PEPTIDOGLYCAN TRANSPEPTIDASE
Ref.: CRYSTAL STRUCTURES OF COMPLEXES OF BACTERIAL DD-PEPTIDASES WITH PEPTIDOGLYCAN-MIMETIC LIGANDS: THE SUBSTRATE SPECIFICITY PUZZLE. J.MOL.BIOL. V. 381 383 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2VGK - REZ C10 H18 N2 O5 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 8 families.
1 2VGK - REZ C10 H18 N2 O5 C[C@H](C(=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 2VGK - REZ C10 H18 N2 O5 C[C@H](C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: REZ; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 REZ 1 1
2 REY 0.517857 0.825
3 NPI 0.511628 0.787879
4 W05 0.491228 0.775
5 I38 0.477273 0.702703
6 MLZ 0.446809 0.609756
7 DLY 0.431818 0.638889
8 DHH 0.422222 0.735294
9 LYS 0.422222 0.621622
10 ALY 0.42 0.810811
11 KKA 0.418182 0.789474
12 REX 0.415385 0.804878
13 API 0.414634 0.757576
14 NLE 0.409091 0.611111
15 26P 0.404255 0.742857
16 ACV 0.403226 0.738095
17 11C 0.4 0.757576
18 UN1 0.4 0.757576
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VGK; Ligand: REZ; 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: 2vgk.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2VGK; Ligand: REZ; 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: 2vgk.bio3) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VGK; Ligand: REZ; 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: 2vgk.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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