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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:

1wdk

2.500 Å

X-ray

2004-05-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-ketoacyl-CoA thiolase
ID:FADA_PSEFR
AC:P28790
Organism:Pseudomonas fragi
Reign:Bacteria
TaxID:296
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:23.990
Number of residues:40
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.053347.625

% Hydrophobic% Polar
66.0233.98
According to VolSite

Ligand :
1wdk_1 Structure
HET Code: ACO
Formula: C23H34N7O17P3S
Molecular weight: 805.539 g/mol
DrugBank ID: -
Buried Surface Area:42.65 %
Polar Surface area: 429.68 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 20

Mass center Coordinates

XYZ
0.48443121.030588.9897


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
O1ANZLYS- 223.880Ionic
(Protein Cationic)
S1PSGCYS- 954.410Hydrophobic
CH3SGCYS- 953.260Hydrophobic
C2PCBMET- 1513.660Hydrophobic
O2BNH1ARG- 2153.34124.68H-Bond
(Protein Donor)
DuArCZARG- 2153.74156.68Pi/Cation
C1BCD2LEU- 2264.210Hydrophobic
CEPCBALA- 22940Hydrophobic
CDPCE2PHE- 2304.150Hydrophobic
CEPCZPHE- 2303.670Hydrophobic
C5BCBALA- 2394.260Hydrophobic
CCPCBALA- 2394.210Hydrophobic
CEPCBALA- 2394.190Hydrophobic
C6PCBSER- 2424.070Hydrophobic
N4POGSER- 2433.38158.62H-Bond
(Ligand Donor)
CAPCG1ILE- 2454.480Hydrophobic
CH3CEMET- 2843.250Hydrophobic
CH3CBALA- 3144.090Hydrophobic
S1PCBALA- 3143.340Hydrophobic
C6PCE1PHE- 3153.910Hydrophobic
C2PCE2PHE- 3153.480Hydrophobic
CH3SGCYS- 3773.580Hydrophobic