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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:

4ffw

2.900 Å

X-ray

2012-06-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dipeptidyl peptidase 4
ID:DPP4_RAT
AC:P14740
Organism:Rattus norvegicus
Reign:Eukaryota
TaxID:10116
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:54.094
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.107344.250

% Hydrophobic% Polar
34.3165.69
According to VolSite

Ligand :
4ffw_1 Structure
HET Code: 715
Formula: C16H16F6N5O
Molecular weight: 408.322 g/mol
DrugBank ID: DB01261
Buried Surface Area:61.69 %
Polar Surface area: 78.66 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
20.7057-9.22153.5259


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
N20OE2GLU- 2033.13173.22H-Bond
(Ligand Donor)
N20OE2GLU- 2033.130Ionic
(Ligand Cationic)
N20OE2GLU- 2042.7125.5H-Bond
(Ligand Donor)
N20OE1GLU- 2042.99168.04H-Bond
(Ligand Donor)
N20OE2GLU- 2042.70Ionic
(Ligand Cationic)
N20OE1GLU- 2042.990Ionic
(Ligand Cationic)
F45CDARG- 3563.780Hydrophobic
F46CBSER- 6314.30Hydrophobic
C5CBTYR- 6324.410Hydrophobic
F9CD2TYR- 6323.410Hydrophobic
F9CG2VAL- 6574.420Hydrophobic
F46CG2VAL- 6573.230Hydrophobic
F9CH2TRP- 6604.30Hydrophobic
N20OHTYR- 6632.97150.1H-Bond
(Ligand Donor)
F46CE1TYR- 6633.790Hydrophobic
F9CE1TYR- 6673.660Hydrophobic
C15CD2TYR- 6674.440Hydrophobic
F46CBVAL- 7124.460Hydrophobic
C1CG2VAL- 7123.720Hydrophobic