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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4edz

2.000 Å

X-ray

2012-03-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Hematopoietic prostaglandin D synthase
ID:HPGDS_HUMAN
AC:O60760
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:26.954
Number of residues:33
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 5
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.590614.250

% Hydrophobic% Polar
54.4045.60
According to VolSite

Ligand :
4edz_1 Structure
HET Code: 0O5
Formula: C23H26N3O2
Molecular weight: 376.471 g/mol
DrugBank ID: -
Buried Surface Area:58.35 %
Polar Surface area: 55.66 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
32.400312.9959-24.484


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C25CD2PHE- 93.880Hydrophobic
C16CEMET- 113.270Hydrophobic
C15CGARG- 144.30Hydrophobic
C7CGARG- 143.830Hydrophobic
C24CGGLN- 364.320Hydrophobic
C1CEMET- 994.430Hydrophobic
C8CGMET- 993.860Hydrophobic
C3CEMET- 993.840Hydrophobic
C10CBMET- 993.340Hydrophobic
C17CE3TRP- 1043.150Hydrophobic
C13CBTRP- 1043.620Hydrophobic
C1CG2ILE- 1553.430Hydrophobic
C3SGCYS- 1564.20Hydrophobic
C17CD1LEU- 1993.960Hydrophobic
O19OHOH- 3782.6126.71H-Bond
(Protein Donor)