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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:

3r2f

2.530 Å

X-ray

2011-03-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Beta-secretase 1
ID:BACE1_HUMAN
AC:P56817
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.23.46


Chains:

Chain Name:Percentage of Residues
within binding site
E100 %


Ligand binding site composition:

B-Factor:21.029
Number of residues:44
Including
Standard Amino Acids: 44
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.886914.625

% Hydrophobic% Polar
27.3172.69
According to VolSite

Ligand :
3r2f_4 Structure
HET Code: PB0
Formula: C36H51F2N4O5
Molecular weight: 657.811 g/mol
DrugBank ID: -
Buried Surface Area:59.74 %
Polar Surface area: 124.58 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 4
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 16

Mass center Coordinates

XYZ
35.532718.297472.8584


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
C25CD1LEU- 303.950Hydrophobic
F47CD2LEU- 303.350Hydrophobic
O44OD1ASP- 323.2175.24H-Bond
(Ligand Donor)
N37OGLY- 342.96162.41H-Bond
(Ligand Donor)
C30CBSER- 354.380Hydrophobic
C17CBTYR- 714.070Hydrophobic
C28CD1TYR- 713.670Hydrophobic
C30CD1TYR- 714.220Hydrophobic
C34CD1TYR- 714.330Hydrophobic
F46CD2TYR- 713.780Hydrophobic
C6CBTYR- 713.340Hydrophobic
C17CBTHR- 724.370Hydrophobic
C31CBTHR- 724.010Hydrophobic
C4CG2THR- 723.630Hydrophobic
O43NTHR- 723.24133.73H-Bond
(Protein Donor)
C31CBGLN- 734.140Hydrophobic
C5CBGLN- 733.870Hydrophobic
F46CD1PHE- 1083.480Hydrophobic
C26CG1ILE- 1104.260Hydrophobic
C35CD1ILE- 1104.340Hydrophobic
F47CD1ILE- 1104.350Hydrophobic
F47CH2TRP- 1153.40Hydrophobic
C28CD1ILE- 1184.340Hydrophobic
C24CD1ILE- 1263.780Hydrophobic
C20CE1TYR- 1984.350Hydrophobic
C24CE1TYR- 1983.760Hydrophobic
C32CE1TYR- 1984.390Hydrophobic
O45OHTYR- 1983.4154.35H-Bond
(Protein Donor)
N37OD1ASP- 22840Ionic
(Ligand Cationic)
N37OD2ASP- 2282.790Ionic
(Ligand Cationic)
N37OD2ASP- 2282.79166.11H-Bond
(Ligand Donor)
N40OGLY- 2302.99156.23H-Bond
(Ligand Donor)
C23CBTHR- 2323.940Hydrophobic
O41NTHR- 2322.98165.63H-Bond
(Protein Donor)
C4CDARG- 2354.410Hydrophobic