Receptor
PDB id Resolution Class Description Source Keywords
4Q6N 1.55 Å NON-ENZYME: OTHER STRUCTURAL ANALYSIS OF THE TRIPEPTIDE-BOUND FORM OF HELICOBA PYLORI CSD4, A D,L-CARBOXYPEPTIDASE HELICOBACTER PYLORI M14 METALLOPEPTIDASE DL-CARBOXYPEPTIDASE PEPTIDOGLYCAN CHYDROLASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION OF MURAMYLTRIP HELICOBACTER PYLORI CSD4, A D,L-CARBOXYPEPTIDASE CO THE HELICAL CELL SHAPE ACTA CRYSTALLOGR.,SECT.D V. 70 2800 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:506;
A:505;
A:507;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MHI A:501;
 Valid;
 none;
 submit data
390.389 C15 H26 N4 O8 C[C@@...
CA A:503;
A:502;
A:504;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D2R 1.9 Å NON-ENZYME: OTHER INHIBITOR BOUND CELL SHAPE DETERMINANT PROTEIN CSD4 FROM HEL PYLORI HELICOBACTER PYLORI MIXED ALPHA BETA SANDWICH CARBOXYPEPTIDASE M14 HYDROLASE-INHIBITOR COMPLEX
Ref.: A BACTERIAL CELL SHAPE-DETERMINING INHIBITOR. ACS CHEM.BIOL. V. 11 981 2016
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 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 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MHI; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 MHI 1 1
2 J0J 0.75 0.971429
3 3KS 0.728814 0.971429
4 KSN 0.465517 0.911765
5 KKA 0.442623 0.815789
6 VB1 0.439394 0.871795
7 3GC 0.431034 0.789474
8 M8F 0.428571 0.809524
9 W05 0.41791 0.894737
10 ACV 0.405797 0.85
11 6X4 0.402597 0.809524
Similar Ligands (3D)
Ligand no: 1; Ligand: MHI; 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 : 5D2R; Ligand: 56W; 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: 5d2r.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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