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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:

3csd

2.290 Å

X-ray

2008-04-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative ketoacyl reductase
ID:ACT3_STRCO
AC:P16544
Organism:Streptomyces coelicolor / M145)
Reign:Bacteria
TaxID:100226
EC Number:1.3.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:38.194
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors: NDP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.445783.000

% Hydrophobic% Polar
54.3145.69
According to VolSite

Ligand :
3csd_1 Structure
HET Code: EMO
Formula: C15H8O5
Molecular weight: 268.221 g/mol
DrugBank ID: DB07715
Buried Surface Area:65.85 %
Polar Surface area: 100.49 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
129.21646.5287-111.264


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
C3CBSER- 1444.40Hydrophobic
O3OGSER- 1442.65132.61H-Bond
(Ligand Donor)
O6OG1THR- 1452.76129.96H-Bond
(Protein Donor)
O3OHTYR- 1572.54166.18H-Bond
(Protein Donor)
C17CD1PHE- 1893.30Hydrophobic
C8CBPHE- 1893.770Hydrophobic
C2SDMET- 1944.090Hydrophobic
C9CG2ILE- 2174.240Hydrophobic
C16CG2ILE- 2173.330Hydrophobic
C10CBARG- 2204.010Hydrophobic
C10CG2VAL- 2214.050Hydrophobic
C8CD2LEU- 2583.640Hydrophobic