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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:

3iex

2.050 Å

X-ray

2009-07-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase
ID:Q9BMI9_SCHMA
AC:Q9BMI9
Organism:Schistosoma mansoni
Reign:Eukaryota
TaxID:6183
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A97 %
B3 %


Ligand binding site composition:

B-Factor:29.052
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.811617.625

% Hydrophobic% Polar
39.8960.11
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3iexHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3iex_1 Structure
HET Code: GMP
Formula: C10H13N5O5
Molecular weight: 283.241 g/mol
DrugBank ID: DB02857
Buried Surface Area:82.16 %
Polar Surface area: 155.22 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-18.73562.08285-29.6333
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3iexRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.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
C3'CE2TYR- 904.170Hydrophobic
O3'OHTYR- 902.93134.27H-Bond
(Protein Donor)
C1'CBALA- 1183.820Hydrophobic
C5'CD1PHE- 1613.570Hydrophobic
C4'CZPHE- 1613.810Hydrophobic
C3'CE1PHE- 1613.550Hydrophobic
C5'CZTYR- 2023.730Hydrophobic
N1OE2GLU- 2033.26124.54H-Bond
(Ligand Donor)
N1OE1GLU- 2032.7160.29H-Bond
(Ligand Donor)
N2OE2GLU- 2032.52166.01H-Bond
(Ligand Donor)
C3'SDMET- 2213.620Hydrophobic
C2'CGMET- 2213.670Hydrophobic
O2'NMET- 2212.89147.7H-Bond
(Protein Donor)
O6ND2ASN- 2452.9165H-Bond
(Protein Donor)
O5'ND1HIS- 2592.75149.65H-Bond
(Protein Donor)