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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:

4lb2

2.800 Å

X-ray

2013-06-20

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
B100 %


Ligand binding site composition:

B-Factor:38.261
Number of residues:21
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1391434.375

% Hydrophobic% Polar
44.7155.29
According to VolSite

Ligand :
4lb2_3 Structure
HET Code: DM5
Formula: C26H26NO9
Molecular weight: 496.486 g/mol
DrugBank ID: DB01177
Buried Surface Area:36.16 %
Polar Surface area: 183.88 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 3
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-16.7889-11.575239.3328


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
C6CGLEU- 1153.620Hydrophobic
C18CGLEU- 1153.620Hydrophobic
C19CD2LEU- 1153.450Hydrophobic
C6'CG1VAL- 1163.570Hydrophobic
O13NZLYS- 1372.7144.46H-Bond
(Protein Donor)
C14CDLYS- 1373.720Hydrophobic
C15CDLYS- 1373.970Hydrophobic
C19CBGLU- 1414.410Hydrophobic
C1CD1ILE- 1423.890Hydrophobic