Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

5dgt

1.080 Å

X-ray

2015-08-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Benzoylformate decarboxylase
ID:MDLC_PSEPU
AC:P20906
Organism:Pseudomonas putida
Reign:Bacteria
TaxID:303
EC Number:4.1.1.7


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:11.485
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: CA

Cavity properties

LigandabilityVolume (Å3)
0.787384.750

% Hydrophobic% Polar
54.3945.61
According to VolSite

Ligand :
5dgt_1 Structure
HET Code: TZD
Formula: C12H15N4O8P2S
Molecular weight: 437.282 g/mol
DrugBank ID: -
Buried Surface Area:63.26 %
Polar Surface area: 238.81 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
13.413742.086825.8137


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
S1CBTHR- 3773.810Hydrophobic
C5BCBTHR- 3774.450Hydrophobic
O22OG1THR- 3772.74145.99H-Bond
(Protein Donor)
O23NSER- 3782.88154.79H-Bond
(Protein Donor)
O23OGSER- 3782.65152.95H-Bond
(Protein Donor)
N4'OGLY- 4012.74169.27H-Bond
(Ligand Donor)
C2ACBLEU- 4034.260Hydrophobic
S1CD1LEU- 4034.20Hydrophobic
C4ACD1LEU- 4033.730Hydrophobic
C5'CD1LEU- 4033.860Hydrophobic
C5BCD1LEU- 4033.820Hydrophobic
N3'NLEU- 4033.17174.9H-Bond
(Protein Donor)
O13NGLY- 4292.83155.65H-Bond
(Protein Donor)
O12NSER- 4302.8150.89H-Bond
(Protein Donor)
O12OGSER- 4302.7151.78H-Bond
(Protein Donor)
C2ACE2TYR- 4333.750Hydrophobic
C4ACZTYR- 4334.50Hydrophobic
C4ACD1TYR- 4583.830Hydrophobic
C5ACD1TYR- 4583.590Hydrophobic
O21NGLY- 4592.82148.46H-Bond
(Protein Donor)
S1CBALA- 46040Hydrophobic
O22NALA- 4602.69154.56H-Bond
(Protein Donor)
C35CD1LEU- 4614.50Hydrophobic
S1CGLEU- 4614.370Hydrophobic
C4ACD1LEU- 4613.740Hydrophobic
C5ACGLEU- 4614.340Hydrophobic
O13CA CA- 6022.220Metal Acceptor
O21CA CA- 6022.270Metal Acceptor