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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:

3fkt

1.900 Å

X-ray

2008-12-17

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
A100 %


Ligand binding site composition:

B-Factor:29.943
Number of residues:35
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.829789.750

% Hydrophobic% Polar
37.1862.82
According to VolSite

Ligand :
3fkt_1 Structure
HET Code: SII
Formula: C28H36FN5O2
Molecular weight: 493.616 g/mol
DrugBank ID: -
Buried Surface Area:59.89 %
Polar Surface area: 79.84 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 4
Rings: 5
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
30.564939.9061-0.156639


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
C5CD2LEU- 503.890Hydrophobic
C10CBTYR- 913.60Hydrophobic
F1CD2TYR- 914.050Hydrophobic
C18CD1TYR- 913.560Hydrophobic
C10CD2TYR- 913.490Hydrophobic
O2NGLN- 932.99151.69H-Bond
(Protein Donor)
C14CBGLN- 933.490Hydrophobic
F1CD1PHE- 1283.650Hydrophobic
N1OPHE- 1282.58164.62H-Bond
(Ligand Donor)
C3CD1ILE- 1304.020Hydrophobic
C9CG1ILE- 1303.410Hydrophobic
C23CZTYR- 2183.740Hydrophobic
C27CD1ILE- 2463.880Hydrophobic
C28CBTHR- 3493.880Hydrophobic
C27CG2VAL- 3523.70Hydrophobic
N2OHOH- 4332.74162.19H-Bond
(Ligand Donor)