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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:

5ewk

1.600 Å

X-ray

2015-11-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative secreted protein
ID:C9Z6T8_STRSW
AC:C9Z6T8
Organism:Streptomyces scabiei
Reign:Bacteria
TaxID:680198
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:30.382
Number of residues:28
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.347374.625

% Hydrophobic% Polar
44.1455.86
According to VolSite

Ligand :
5ewk_1 Structure
HET Code: P34
Formula: C17H18N3O2
Molecular weight: 296.344 g/mol
DrugBank ID: DB08348
Buried Surface Area:58.92 %
Polar Surface area: 62.64 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
23.311233.07120.6642


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
OADNSER- 782.81154.71H-Bond
(Protein Donor)
NANOSER- 782.83166.14H-Bond
(Ligand Donor)
OND2ASN- 1102.95141.46H-Bond
(Protein Donor)
CATCBSER- 1173.420Hydrophobic
CAICBSER- 1173.270Hydrophobic
CAHCBTHR- 1193.950Hydrophobic
CAHCD2LEU- 1243.60Hydrophobic
CAECBGLN- 1584.110Hydrophobic
CAFCGGLU- 1603.690Hydrophobic