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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:

2npf

2.900 Å

X-ray

2006-10-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Elongation factor 2
ID:EF2_YEAST
AC:P32324
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:38.305
Number of residues:41
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.201627.750

% Hydrophobic% Polar
55.9144.09
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2npfHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2npf_1 Structure
HET Code: MOU
Formula: C37H52O12
Molecular weight: 688.802 g/mol
DrugBank ID: -
Buried Surface Area:62.17 %
Polar Surface area: 180.77 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 1
Rings: 6
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 15

Mass center Coordinates

XYZ
2.9005715.197641.902
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2npfRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


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
C2CBPRO- 4873.930Hydrophobic
C41CGGLN- 4903.620Hydrophobic
C43CGGLN- 4904.370Hydrophobic
C2CD2LEU- 5193.90Hydrophobic
C36CD2LEU- 5194.180Hydrophobic
C31CD2LEU- 5194.350Hydrophobic
C22CE1TYR- 5214.060Hydrophobic
C26CE1TYR- 5213.920Hydrophobic
C28CZTYR- 5213.940Hydrophobic
C30CZTYR- 5213.670Hydrophobic
C34CGTYR- 5213.980Hydrophobic
C22CBSER- 5234.380Hydrophobic
C14CBGLU- 5244.210Hydrophobic
O24NGLU- 5242.77152.25H-Bond
(Protein Donor)
O25NGLU- 5243.36146.49H-Bond
(Protein Donor)
C22CG1ILE- 5293.990Hydrophobic
C39CBALA- 5314.490Hydrophobic
C21CBPRO- 5594.030Hydrophobic
C22CBPRO- 5594.270Hydrophobic
C21CG2VAL- 5614.30Hydrophobic
O12NALA- 5622.84174.15H-Bond
(Protein Donor)
C7CBPRO- 7273.520Hydrophobic
C6CE1PHE- 7294.170Hydrophobic
C32CE1PHE- 7294.390Hydrophobic
C21CG1VAL- 7744.140Hydrophobic
C7CG2VAL- 7744.120Hydrophobic
C43CBSER- 7774.470Hydrophobic
C44CBPHE- 7804.40Hydrophobic
C44CG2THR- 7813.920Hydrophobic
O46NTHR- 7813.02138.88H-Bond
(Protein Donor)
C38CGMET- 7964.340Hydrophobic
C40CGMET- 7963.620Hydrophobic
C6CBPHE- 7984.280Hydrophobic
C7CD1PHE- 79840Hydrophobic
C13CBPHE- 7983.920Hydrophobic
C17CE2PHE- 7983.830Hydrophobic
C18CZPHE- 7984.280Hydrophobic
C16CD2PHE- 7983.640Hydrophobic
O33NPHE- 7983.21169.14H-Bond
(Protein Donor)
C18CZ2TRP- 8013.460Hydrophobic