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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:

2aqb

2.190 Å

X-ray

2005-08-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-oxoacyl-[acyl-carrier-protein] synthase 1
ID:FABB_ECOLI
AC:P0A953
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:2.3.1.41


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:15.493
Number of residues:29
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.502523.125

% Hydrophobic% Polar
60.0040.00
According to VolSite

Ligand :
2aqb_3 Structure
HET Code: TL6
Formula: C10H11O2S
Molecular weight: 195.258 g/mol
DrugBank ID: DB08628
Buried Surface Area:76.61 %
Polar Surface area: 65.42 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-4.2059240.547230.1121


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
S1SGCYS- 1633.980Hydrophobic
C9CD2PHE- 2293.680Hydrophobic
C10CGPRO- 2723.760Hydrophobic
O1NE2HIS- 2982.92131.04H-Bond
(Protein Donor)
C9CBTHR- 3003.770Hydrophobic
C9CG2THR- 3023.70Hydrophobic
O1NE2HIS- 3333.25143.31H-Bond
(Protein Donor)
S1CD1PHE- 3924.280Hydrophobic
C4CE1PHE- 3924.110Hydrophobic
C9CZPHE- 3924.390Hydrophobic