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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:

3roe

2.110 Å

X-ray

2011-04-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NAD(P)H-hydrate epimerase
ID:NNRE_MOUSE
AC:Q8K4Z3
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:5.1.99.6


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:51.014
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.567661.500

% Hydrophobic% Polar
47.4552.55
According to VolSite

Ligand :
3roe_3 Structure
HET Code: THM
Formula: C10H14N2O5
Molecular weight: 242.229 g/mol
DrugBank ID: DB04485
Buried Surface Area:69.16 %
Polar Surface area: 99.1 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-1.0129424.996378.2961


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
C5MCBALA- 354.240Hydrophobic
C5MCG1VAL- 383.620Hydrophobic
C5MCBASP- 394.070Hydrophobic
O3'OLEU- 533.46163.5H-Bond
(Ligand Donor)
C3'CBALA- 574.030Hydrophobic
C5'CBASN- 893.810Hydrophobic
O5'OD2ASP- 932.75170.48H-Bond
(Protein Donor)
N3OD2ASP- 1882.99160.71H-Bond
(Ligand Donor)
C1'CG2THR- 2124.490Hydrophobic
C5MCG2THR- 2124.270Hydrophobic
O4NZLYS- 2152.53171.58H-Bond
(Protein Donor)
C2'CZPHE- 2324.120Hydrophobic