Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

5dw6

1.550 Å

X-ray

2015-09-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Succinyl-CoA:acetate CoA-transferase
ID:SCACT_ACEAC
AC:B3EY95
Organism:Acetobacter aceti
Reign:Bacteria
TaxID:435
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:14.658
Number of residues:54
Including
Standard Amino Acids: 47
Non Standard Amino Acids: 0
Water Molecules: 7
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.988634.500

% Hydrophobic% Polar
42.5557.45
According to VolSite

Ligand :
5dw6_1 Structure
HET Code: 0T1
Formula: C22H34N7O16P3
Molecular weight: 745.464 g/mol
DrugBank ID: -
Buried Surface Area:45.01 %
Polar Surface area: 387.31 Å2
Number of
H-Bond Acceptors: 20
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 18

Mass center Coordinates

XYZ
-6.6350813.7097-25.8515


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C6PCE1PHE- 923.880Hydrophobic
C1PCGGLN- 2674.260Hydrophobic
C1PCGGLU- 2943.860Hydrophobic
N6AOILE- 3642.79136.44H-Bond
(Ligand Donor)
CDPCD1ILE- 3644.110Hydrophobic
CEPCD1ILE- 3644.050Hydrophobic
C1BCEMET- 3834.170Hydrophobic
C4BSDMET- 3834.210Hydrophobic
CEPCGMET- 3833.740Hydrophobic
O9PND2ASN- 3842.83166.97H-Bond
(Protein Donor)
C2PCBSER- 3894.460Hydrophobic
C1PCD2PHE- 3923.880Hydrophobic
O7ANZLYS- 4083.840Ionic
(Protein Cationic)
O5POHOH- 7582.64179.97H-Bond
(Protein Donor)
O9POHOH- 7942.78139.34H-Bond
(Protein Donor)
N6AOHOH- 8013.01163.97H-Bond
(Ligand Donor)
O5AOHOH- 8433.08179.97H-Bond
(Protein Donor)
N4POHOH- 9232.83156.8H-Bond
(Ligand Donor)