Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IOD A:514;
A:518;
A:519;
A:506;
A:522;
A:515;
A:511;
A:504;
A:510;
A:516;
A:507;
A:513;
A:520;
A:508;
A:512;
A:521;
A:517;
A:505;
A:509;
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;
submit data
126.904 I [I-]
ZN A:501;
A:502;
A:503;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
56W A:523;
Valid;
none;
Ki = 1.5 uM
396.33 C14 H25 N2 O9 P CC(=O...
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 1256 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 1068 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 922 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
Ligand no: 1; Ligand: 56W; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 56W 1 1
2 BIX 0.451613 0.863636
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D2R; Ligand: 56W; Similar sites found: 16
This union binding pocket(no: 1) in the query (biounit: 5d2r.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NSA BEN 0.007573 0.43707 1.51899
2 4UIB GWX 0.000002228 0.47779 1.9544
3 1PCA VAL 0.00003228 0.40775 3.22581
4 5TO8 7FM 0.01829 0.40449 3.5461
5 4OOE NDP 0.02818 0.41908 3.64465
6 4OOE FOM 0.02818 0.41908 3.64465
7 7CPA FVF 0.00000005061 0.63014 3.90879
8 5EFQ ADP 0.004462 0.40405 4.03458
9 3NFZ 3NF 0.009335 0.41374 5.50459
10 4A38 BZS 0.000000468 0.47774 5.6701
11 4P10 2B8 0.000002707 0.52055 6.18812
12 2V77 PAY 0.0000106 0.49739 7.11974
13 3KRR DQX 0.04782 0.40035 8.13559
14 2BO9 VAL 0.000005812 0.46783 10.0649
15 2PCU ASP 0.00001005 0.47003 10.1639
16 1DTD GLU 0.00004398 0.41452 21.3115
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