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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:

2icx

1.850 Å

X-ray

2006-09-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UTP--glucose-1-phosphate uridylyltransferase 2
ID:UGPA2_ARATH
AC:Q9M9P3
Organism:Arabidopsis thaliana
Reign:Eukaryota
TaxID:3702
EC Number:2.7.7.9


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:6.772
Number of residues:31
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.010573.750

% Hydrophobic% Polar
29.4170.59
According to VolSite

Ligand :
2icx_1 Structure
HET Code: UTP
Formula: C9H11N2O15P3
Molecular weight: 480.109 g/mol
DrugBank ID: DB04005
Buried Surface Area:52.83 %
Polar Surface area: 299.67 Å2
Number of
H-Bond Acceptors: 15
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-10.581-1.27417-33.0679


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
C4'CD1LEU- 854.080Hydrophobic
C1'CBLEU- 853.670Hydrophobic
C3'CBLEU- 854.320Hydrophobic
O3'OLEU- 852.83136.33H-Bond
(Ligand Donor)
O2NGLY- 872.92139.25H-Bond
(Protein Donor)
O2BNZLYS- 992.66123.58H-Bond
(Protein Donor)
O2BNZLYS- 992.660Ionic
(Protein Cationic)
N3OE1GLN- 1622.94167.05H-Bond
(Ligand Donor)
C4'CBASN- 2204.070Hydrophobic
O3'NSER- 2213.27147H-Bond
(Protein Donor)
O3ANZLYS- 3603.08122.99H-Bond
(Protein Donor)
O2BNZLYS- 3602.74166.09H-Bond
(Protein Donor)
O2BNZLYS- 3602.740Ionic
(Protein Cationic)
O3GOHOH- 10303.06179.97H-Bond
(Protein Donor)