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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:

2w6n

1.870 Å

X-ray

2008-12-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Biotin carboxylase
ID:ACCC_ECOLI
AC:P24182
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:6.3.4.14


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.114
Number of residues:35
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0171211.625

% Hydrophobic% Polar
39.5560.45
According to VolSite

Ligand :
2w6n_1 Structure
HET Code: OA2
Formula: C18H17N3O2
Molecular weight: 307.346 g/mol
DrugBank ID: DB08315
Buried Surface Area:62.44 %
Polar Surface area: 72.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
3.39096-22.129123.9202


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
C19CD1ILE- 1573.510Hydrophobic
O2NZLYS- 1592.85155.03H-Bond
(Protein Donor)
C19SDMET- 1693.840Hydrophobic
C21CG2VAL- 1713.960Hydrophobic
N8OE2GLU- 2012.87162.88H-Bond
(Ligand Donor)
N8OLYS- 2022.78159.89H-Bond
(Ligand Donor)
N7NLEU- 2043.01176.33H-Bond
(Protein Donor)
C15CBHIS- 2094.10Hydrophobic
C14CGGLN- 2334.410Hydrophobic
C12CD2LEU- 2783.940Hydrophobic
C17CG2ILE- 4373.920Hydrophobic
C20CD1ILE- 4374.10Hydrophobic
C12CD1ILE- 4374.250Hydrophobic