scPDB - 2icy entry

Protein Data Bank Entry:

PDB ID : 2icy

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2006-09-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	18.781
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.195	664.875

% Hydrophobic	% Polar
31.98	68.02
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	57.98 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
13.7384	-18.4329	30.3569

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O3C	O	LEU- 85	2.94	150.81	H-Bond (Ligand Donor)	false
C1C	CB	LEU- 85	3.25	0	Hydrophobic	false
C4C	CD1	LEU- 85	3.58	0	Hydrophobic	false
O2	N	GLY- 87	3.48	134.04	H-Bond (Protein Donor)	false
O2C	N	GLY- 87	3.35	124.66	H-Bond (Protein Donor)	false
O2C	N	GLY- 88	3.36	128.17	H-Bond (Protein Donor)	false
N3	OE1	GLN- 162	2.96	174.38	H-Bond (Ligand Donor)	false
O4	N	GLY- 191	3.19	125.97	H-Bond (Protein Donor)	false
O1B	NE2	HIS- 192	3.12	154.58	H-Bond (Protein Donor)	false
C5C	CB	ASN- 220	4.1	0	Hydrophobic	false
C4C	CB	ASN- 220	3.96	0	Hydrophobic	false
O5'	ND2	ASN- 220	3.28	175.35	H-Bond (Protein Donor)	false
O3C	N	SER- 221	3.19	153.85	H-Bond (Protein Donor)	false
C4'	CB	ASN- 293	3.7	0	Hydrophobic	false
C6'	CB	ASN- 295	3.55	0	Hydrophobic	false
C4'	CB	ASN- 295	3.53	0	Hydrophobic	false
C6'	CE1	PHE- 356	3.52	0	Hydrophobic	false