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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:

4xp1

2.890 Å

X-ray

2015-01-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Sodium-dependent dopamine transporter
ID:DAT_DROME
AC:Q7K4Y6
Organism:Drosophila melanogaster
Reign:Eukaryota
TaxID:7227
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:67.661
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1651326.375

% Hydrophobic% Polar
50.8949.11
According to VolSite

Ligand :
4xp1_1 Structure
HET Code: LDP
Formula: C8H12NO2
Molecular weight: 154.186 g/mol
DrugBank ID: DB00988
Buried Surface Area:72.38 %
Polar Surface area: 68.1 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 3
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-10.73893.75618-25.2801


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
C7CE1PHE- 434.140Hydrophobic
N1OD2ASP- 463.12121.12H-Bond
(Ligand Donor)
N1OD2ASP- 463.120Ionic
(Ligand Cationic)
C5CBALA- 1174.30Hydrophobic
O2OALA- 1172.86132.65H-Bond
(Ligand Donor)
C2CG1VAL- 1203.730Hydrophobic
C4CG1VAL- 1203.580Hydrophobic
O1OD1ASP- 1212.79164.04H-Bond
(Ligand Donor)
C3CBTYR- 1244.290Hydrophobic
C7CZPHE- 3254.360Hydrophobic
C6CD1PHE- 3253.370Hydrophobic