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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:

1yrd

1.700 Å

X-ray

2005-02-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Camphor 5-monooxygenase
ID:CPXA_PSEPU
AC:P00183
Organism:Pseudomonas putida
Reign:Bacteria
TaxID:303
EC Number:1.14.15.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:14.681
Number of residues:19
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.692793.125

% Hydrophobic% Polar
59.1540.85
According to VolSite

Ligand :
1yrd_1 Structure
HET Code: CAM
Formula: C10H16O
Molecular weight: 152.233 g/mol
DrugBank ID: DB01744
Buried Surface Area:78.03 %
Polar Surface area: 17.07 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 0
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
16.758913.292241.0065


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
C10CZPHE- 874.10Hydrophobic
OOHTYR- 962.7155.9H-Bond
(Protein Donor)
C3CG2THR- 1014.090Hydrophobic
C10CG2THR- 1854.090Hydrophobic
C5CD1LEU- 2443.670Hydrophobic
C10CG1VAL- 2473.690Hydrophobic
C6CG2THR- 2524.440Hydrophobic
C9CG2THR- 2524.170Hydrophobic
C8CG1VAL- 2953.550Hydrophobic
C8CG2ILE- 3954.220Hydrophobic
C10CG2ILE- 3954.280Hydrophobic
C9CG2VAL- 3964.070Hydrophobic
C10CG2VAL- 3964.110Hydrophobic