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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:

3mw9

2.400 Å

X-ray

2010-05-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutamate dehydrogenase 1, mitochondrial
ID:DHE3_BOVIN
AC:P00366
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:1.4.1.3


Chains:

Chain Name:Percentage of Residues
within binding site
B45 %
C55 %


Ligand binding site composition:

B-Factor:48.821
Number of residues:44
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0591329.750

% Hydrophobic% Polar
35.0364.97
According to VolSite

Ligand :
3mw9_6 Structure
HET Code: NAI
Formula: C21H27N7O14P2
Molecular weight: 663.425 g/mol
DrugBank ID: DB00157
Buried Surface Area:60.64 %
Polar Surface area: 342.9 Å2
Number of
H-Bond Acceptors: 19
H-Bond Donors: 6
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
25.891528.033531.81


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
C6NCDARG- 864.10Hydrophobic
C4NCGARG- 863.960Hydrophobic
C5NCBPRO- 1213.20Hydrophobic
C6NCGPRO- 1213.910Hydrophobic
C5BCG2ILE- 2033.980Hydrophobic
O3DNHIS- 3913.13131.17H-Bond
(Protein Donor)
C5DCBSER- 3934.360Hydrophobic
N1AOHOH- 7263.18170.27H-Bond
(Ligand Donor)