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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:

2w71

1.990 Å

X-ray

2008-12-19

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:29.148
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.900675.000

% Hydrophobic% Polar
42.5057.50
According to VolSite

Ligand :
2w71_1 Structure
HET Code: L23
Formula: C15H14Cl2N5
Molecular weight: 335.211 g/mol
DrugBank ID: DB08076
Buried Surface Area:67.77 %
Polar Surface area: 70.87 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
35.846123.04323.2845


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
N4NZLYS- 1592.85157.67H-Bond
(Protein Donor)
DuArNZLYS- 1593.96101.59Pi/Cation
C12CEMET- 1694.150Hydrophobic
N14OE2GLU- 2013.09177.15H-Bond
(Ligand Donor)
N14OLYS- 2022.78163.12H-Bond
(Ligand Donor)
N13NLEU- 2042.94169.29H-Bond
(Protein Donor)
C20CBHIS- 2094.210Hydrophobic
C22CGGLN- 2333.80Hydrophobic
CL21CD2LEU- 2784.440Hydrophobic
C6CD1LEU- 2783.720Hydrophobic
CL21CD1ILE- 2873.60Hydrophobic
C12CD1ILE- 2873.920Hydrophobic
C20CG2ILE- 4373.910Hydrophobic
C22CBILE- 4373.570Hydrophobic
C18CD1ILE- 4373.730Hydrophobic