Receptor
PDB id Resolution Class Description Source Keywords
4WCN 1.75 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF TRIPEPTIDE BOUND CELL SHAPE DETERMINANT PROTEIN FROM HELICOBACTER PYLORI HELICOBACTER PYLORI MIXED ALPHA BETA SANDWICH CARBOXYPEPTIDASE M14 HYDROLASE
Ref.: HELICAL SHAPE OF HELICOBACTER PYLORI REQUIRES AN AT GLUTAMINE AS A ZINC LIGAND IN THE CARBOXYPEPTIDASE J.BIOL.CHEM. V. 290 3622 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IOD A:517;
A:521;
A:540;
A:503;
A:536;
A:530;
A:535;
A:532;
A:518;
A:508;
A:539;
A:509;
A:523;
A:528;
A:506;
A:538;
A:531;
A:515;
A:522;
A:501;
A:520;
A:513;
A:505;
A:525;
A:512;
A:541;
A:516;
A:524;
A:534;
A:511;
A:507;
A:533;
A:526;
A:537;
A:519;
A:510;
A:502;
A:529;
A:514;
A:527;
A:504;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
126.904 I [I-]
NA A:543;
A:544;
 Invalid;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
ZN A:542;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
3KS A:545;
 Valid;
 none;
 submit data
432.426 C17 H28 N4 O9 C[C@@...
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: 3KS; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 3KS 1 1
2 MHI 0.728814 0.971429
3 J0J 0.585714 1
4 6X4 0.461538 0.833333
5 MXG 0.43 0.614035
6 KSN 0.421875 0.885714
7 KKA 0.402985 0.794872
8 VB1 0.402778 0.85
9 W05 0.402778 0.871795
Similar Ligands (3D)
Ligand no: 1; Ligand: 3KS; 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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