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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:

1ek5

1.800 Å

X-ray

2000-03-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-glucose 4-epimerase
ID:GALE_HUMAN
AC:Q14376
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:22.889
Number of residues:47
Including
Standard Amino Acids: 44
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9971451.250

% Hydrophobic% Polar
36.5163.49
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1ek5HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1ek5_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:75.7 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
-2.5353913.977755.1453
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1ek5RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
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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
O2ANTYR- 132.88176.05H-Bond
(Protein Donor)
O2NNILE- 142.74178.1H-Bond
(Protein Donor)
C3NCD1ILE- 144.280Hydrophobic
O3BOD1ASP- 332.5153.99H-Bond
(Ligand Donor)
O3BOD2ASP- 333.09128.11H-Bond
(Ligand Donor)
O2BOD2ASP- 332.68162.89H-Bond
(Ligand Donor)
N3ANASN- 343.31138.56H-Bond
(Protein Donor)
C2BCBHIS- 364.350Hydrophobic
O1AND2ASN- 372.93167.12H-Bond
(Protein Donor)
O2BNASN- 372.7152.77H-Bond
(Protein Donor)
C2BCBASN- 373.860Hydrophobic
N6AOD1ASP- 662.73150.55H-Bond
(Ligand Donor)
N1ANILE- 673.28165.65H-Bond
(Protein Donor)
C4DCBPHE- 884.170Hydrophobic
O1ANZLYS- 923.810Ionic
(Protein Cationic)
O3NZLYS- 923.49121.94H-Bond
(Protein Donor)
C5DCGLYS- 924.410Hydrophobic
C2DCBLYS- 923.690Hydrophobic
O3DOSER- 1303.47148.46H-Bond
(Ligand Donor)
C5NCBSER- 1323.940Hydrophobic
C2DCZTYR- 1574.340Hydrophobic
O2DNZLYS- 1612.75169.65H-Bond
(Protein Donor)
C5NCE2TYR- 1853.290Hydrophobic
C3NCGPRO- 1884.20Hydrophobic
O5BOHOH- 6013.13153.2H-Bond
(Protein Donor)
O7NOHOH- 6582.74179.96H-Bond
(Protein Donor)