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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:

4f32

1.900 Å

X-ray

2012-05-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-oxoacyl-[acyl-carrier-protein] synthase 2
ID:A4JL30_BURVG
AC:A4JL30
Organism:Burkholderia vietnamiensis )
Reign:Bacteria
TaxID:269482
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:7.519
Number of residues:34
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.064452.250

% Hydrophobic% Polar
44.0355.97
According to VolSite

Ligand :
4f32_2 Structure
HET Code: N32
Formula: C24H26NO6
Molecular weight: 424.466 g/mol
DrugBank ID: -
Buried Surface Area:59.59 %
Polar Surface area: 126.76 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 4
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
5.296194.24071-44.4764


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
C28CBARG- 2154.40Hydrophobic
C18CBALA- 2164.40Hydrophobic
N28OTHR- 2802.78176.1H-Bond
(Ligand Donor)
C2CBALA- 2814.350Hydrophobic
O20OG1THR- 3172.73174.09H-Bond
(Protein Donor)
C3CBTHR- 3174.110Hydrophobic
O19NVAL- 3192.99155.92H-Bond
(Protein Donor)
C2CBVAL- 3194.20Hydrophobic
O32NE2HIS- 3493.2124.12H-Bond
(Protein Donor)
O33NE2HIS- 3492.67167.79H-Bond
(Protein Donor)
C26CBPHE- 4074.150Hydrophobic