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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:

1zly

2.070 Å

X-ray

2005-05-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Trifunctional purine biosynthetic protein adenosine-3
ID:PUR2_HUMAN
AC:P22102
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.1.2.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:56.962
Number of residues:30
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.501307.125

% Hydrophobic% Polar
48.3551.65
According to VolSite

Ligand :
1zly_1 Structure
HET Code: DQB
Formula: C20H20N5O4
Molecular weight: 394.404 g/mol
DrugBank ID: -
Buried Surface Area:54.5 %
Polar Surface area: 148.73 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
34.587237.126136.0439


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
C7CD2LEU- 853.990Hydrophobic
C6CD2LEU- 853.990Hydrophobic
OE1CZARG- 903.980Ionic
(Protein Cationic)
OE1NH2ARG- 903.12151.02H-Bond
(Protein Donor)
OE1NILE- 912.99160.21H-Bond
(Protein Donor)
C8CBILE- 914.290Hydrophobic
C15CG1ILE- 914.060Hydrophobic
N1NLEU- 923.28145.97H-Bond
(Protein Donor)
C8CGLEU- 924.110Hydrophobic
C14CBSER- 1184.260Hydrophobic
C4ACG1VAL- 1393.950Hydrophobic
N3OALA- 1402.63133.31H-Bond
(Ligand Donor)
NA2OALA- 1402.96124.94H-Bond
(Ligand Donor)
NA2OGLU- 1412.94126.13H-Bond
(Ligand Donor)
C16CG1VAL- 1433.650Hydrophobic
C4ACG1VAL- 1434.430Hydrophobic
OA4NASP- 1442.7143.3H-Bond
(Protein Donor)
OA4OHOH- 14622.52179.95H-Bond
(Protein Donor)
N10OHOH- 15242.8143.88H-Bond
(Ligand Donor)