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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:

4l9k

2.400 Å

X-ray

2013-06-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serum albumin
ID:ALBU_HUMAN
AC:P02768
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A96 %
B4 %


Ligand binding site composition:

B-Factor:46.397
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.3892136.375

% Hydrophobic% Polar
40.7659.24
According to VolSite

Ligand :
4l9k_1 Structure
HET Code: EHF
Formula: C20H17N2O5
Molecular weight: 365.359 g/mol
DrugBank ID: -
Buried Surface Area:59.91 %
Polar Surface area: 113.79 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-9.15593-7.421898.81463


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
C19CBLEU- 1154.270Hydrophobic
C19CBARG- 1174.110Hydrophobic
O22NEARG- 1172.86165.63H-Bond
(Protein Donor)
O23NH2ARG- 1173.22162.02H-Bond
(Protein Donor)
O22CZARG- 1173.720Ionic
(Protein Cationic)
O23CZARG- 1173.980Ionic
(Protein Cationic)
C26CD1TYR- 1384.170Hydrophobic
C26CE1TYR- 1613.860Hydrophobic
C19CDARG- 1864.370Hydrophobic
O27NH2ARG- 1862.65145.28H-Bond
(Protein Donor)