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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:

4fk3

2.650 Å

X-ray

2012-06-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serine/threonine-protein kinase B-raf
ID:BRAF_HUMAN
AC:P15056
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:32.932
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.051715.500

% Hydrophobic% Polar
56.6043.40
According to VolSite

Ligand :
4fk3_1 Structure
HET Code: 325
Formula: C21H16F2N4O3S
Molecular weight: 442.439 g/mol
DrugBank ID: DB07000
Buried Surface Area:62.79 %
Polar Surface area: 113.19 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-1.9853550.204120.1495


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
C6CG2ILE- 4634.120Hydrophobic
F29CG1VAL- 4713.430Hydrophobic
C11CG1VAL- 4714.430Hydrophobic
C11CBALA- 4814.420Hydrophobic
F29CBALA- 4813.550Hydrophobic
C19CBLYS- 4833.410Hydrophobic
C26CD1LEU- 5053.780Hydrophobic
C31CD2LEU- 5053.760Hydrophobic
C31CD2LEU- 5144.260Hydrophobic
C22CD2LEU- 5143.490Hydrophobic
C26CG2ILE- 5274.360Hydrophobic
C20CG2ILE- 5273.90Hydrophobic
C26CG2THR- 5293.970Hydrophobic
C20CG2THR- 5293.780Hydrophobic
N15OGLN- 5303.18157.1H-Bond
(Ligand Donor)
N9NCYS- 5323.1146.66H-Bond
(Protein Donor)
F28CE1PHE- 5833.540Hydrophobic
C31CE2PHE- 5953.780Hydrophobic
O27NPHE- 5952.99155.28H-Bond
(Protein Donor)
O27NGLY- 5963.26124.69H-Bond
(Protein Donor)