Receptor
PDB id Resolution Class Description Source Keywords
6QBH 1.85 Å EC: 3.4.23.5 CRYSTAL STRUCTURE OF HUMAN CATHEPSIN D IN COMPLEX WITH MACRO INHIBITOR 33 HOMO SAPIENS ASPARTIC PROTEASE PEPTIDOMIMETIC INHIBITOR HYDROLASE
Ref.: BIOMIMETIC MACROCYCLIC INHIBITORS OF HUMAN CATHEPSI STRUCTURE-ACTIVITY RELATIONSHIP AND BINDING MODE AN J.MED.CHEM. V. 63 1576 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS B:403;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S CS(=O...
S43 A:103;
 Valid;
 none;
 ic50 = 2.5 nM
503.674 C28 H45 N3 O5 CC(C)...
NAG NAG C:1;
 Invalid;
 none;
 submit data
408.404 n/a O=C(N...
NAG B:401;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
SO4 B:402;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1LYB 2.5 Å EC: 3.4.23.5 CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CA IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN HOMO SAPIENS LYSOSOMAL ASPARTIC PROTEASE HYDROLASE-HYDROLASE INHIBITOR C
Ref.: CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING A DESIGN. PROC.NATL.ACAD.SCI.USA V. 90 6796 1993
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6QCB ic50 = 5.8 nM HWE C28 H45 N3 O4 CC(C)[C@H]....
2 6QBH ic50 = 2.5 nM S43 C28 H45 N3 O5 CC(C)[C@H]....
3 6QBG ic50 = 0.6 nM HVT C32 H47 N3 O4 CC(C)[C@H]....
4 1LYB Ki = 3.8 pM IVA VAL VAL STA ALA STA n/a n/a
5 4OD9 ic50 = 58 nM 2RZ C29 H34 N4 O6 [H]/N=C(N[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6QCB ic50 = 5.8 nM HWE C28 H45 N3 O4 CC(C)[C@H]....
2 6QBH ic50 = 2.5 nM S43 C28 H45 N3 O5 CC(C)[C@H]....
3 6QBG ic50 = 0.6 nM HVT C32 H47 N3 O4 CC(C)[C@H]....
4 1LYB Ki = 3.8 pM IVA VAL VAL STA ALA STA n/a n/a
5 4OD9 ic50 = 58 nM 2RZ C29 H34 N4 O6 [H]/N=C(N[....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6QCB ic50 = 5.8 nM HWE C28 H45 N3 O4 CC(C)[C@H]....
2 6QBH ic50 = 2.5 nM S43 C28 H45 N3 O5 CC(C)[C@H]....
3 6QBG ic50 = 0.6 nM HVT C32 H47 N3 O4 CC(C)[C@H]....
4 1LYB Ki = 3.8 pM IVA VAL VAL STA ALA STA n/a n/a
5 4OD9 ic50 = 58 nM 2RZ C29 H34 N4 O6 [H]/N=C(N[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: S43; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 S43 1 1
2 HWE 0.714286 0.910714
3 HVT 0.53 0.864407
Similar Ligands (3D)
Ligand no: 1; Ligand: S43; 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 : 1LYB; Ligand: IVA VAL VAL STA ALA STA; 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: 1lyb.bio3) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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