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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:

2v5a

2.310 Å

X-ray

2008-10-02

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:29.187
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7011161.000

% Hydrophobic% Polar
37.2162.79
According to VolSite

Ligand :
2v5a_1 Structure
HET Code: LZL
Formula: C17H15N5
Molecular weight: 289.334 g/mol
DrugBank ID: DB08146
Buried Surface Area:62.91 %
Polar Surface area: 67.93 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
4.86091-22.767524.1655


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
N18NZLYS- 1592.84145.13H-Bond
(Protein Donor)
N6NZLYS- 1593.17141.03H-Bond
(Protein Donor)
C1CEMET- 1694.280Hydrophobic
N22OE2GLU- 2013.2158.61H-Bond
(Ligand Donor)
N22OLYS- 2022.73158.98H-Bond
(Ligand Donor)
N20NLEU- 2043.18164.53H-Bond
(Protein Donor)
C19CGGLN- 2333.970Hydrophobic
C9CD1LEU- 2783.470Hydrophobic
C7CD2LEU- 2784.310Hydrophobic
C4CD2LEU- 2783.880Hydrophobic
C13CG2ILE- 4373.920Hydrophobic
C3CD1ILE- 4373.630Hydrophobic