Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4kwi

2.000 Å

X-ray

2013-05-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Reductase homolog
ID:Q9ZGC1_STRCY
AC:Q9ZGC1
Organism:Streptomyces cyanogenus
Reign:Bacteria
TaxID:80860
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:29.913
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.415749.250

% Hydrophobic% Polar
62.1637.84
According to VolSite

Ligand :
4kwi_2 Structure
HET Code: 1TJ
Formula: C19H11O5
Molecular weight: 319.288 g/mol
DrugBank ID: -
Buried Surface Area:62.06 %
Polar Surface area: 94.5 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
3.25125-11.076-10.7256


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
CAMCEMET- 1014.430Hydrophobic
CAKSDMET- 1014.330Hydrophobic
CAASDMET- 1033.640Hydrophobic
OAFNGLY- 1483.24123.53H-Bond
(Protein Donor)
CATCD1LEU- 1493.890Hydrophobic
CAICD2LEU- 1493.520Hydrophobic
CAXCGLEU- 1493.610Hydrophobic
CAGCG2VAL- 1523.740Hydrophobic
OAENE2GLN- 1572.98149.05H-Bond
(Protein Donor)
CAACG1VAL- 2054.170Hydrophobic
CAKCD1LEU- 2094.110Hydrophobic
CAQCD2LEU- 2093.740Hydrophobic
CASCD2LEU- 2093.660Hydrophobic
CAGCD2LEU- 2123.960Hydrophobic
CAICD1LEU- 2123.630Hydrophobic
CAHCG2THR- 2503.540Hydrophobic