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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:

5c3r

2.350 Å

X-ray

2015-06-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thymine dioxygenase
ID:Q7RYZ9_NEUCR
AC:Q7RYZ9
Organism:Neurospora crassa
Reign:Eukaryota
TaxID:367110
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:27.236
Number of residues:16
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.438732.375

% Hydrophobic% Polar
45.6254.38
According to VolSite

Ligand :
5c3r_3 Structure
HET Code: HMU
Formula: C5H6N2O3
Molecular weight: 142.113 g/mol
DrugBank ID: -
Buried Surface Area:60 %
Polar Surface area: 78.42 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 3
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-27.048760.5152-24.5644


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
O2ND2ASN- 873.18160.36H-Bond
(Protein Donor)
CM5CBASP- 2164.430Hydrophobic
O4NTYR- 2172.78165.19H-Bond
(Protein Donor)
CM5CZTYR- 2174.180Hydrophobic
CM5CE1PHE- 2924.120Hydrophobic