scPDB - 2vce entry

Protein Data Bank Entry:

PDB ID : 2vce

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-09-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-glycosyltransferase 72B1
ID:	U72B1_ARATH
AC:	Q9M156
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	13.095
Number of residues:	49
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.896	955.125

% Hydrophobic	% Polar
42.05	57.95
According to VolSite

Ligand :

HET Code:	U2F
Formula:	C15H21FN2O16P2
Molecular weight:	566.277 g/mol
DrugBank ID:	DB03488
Buried Surface Area:	78.18 %
Polar Surface area:	296.59 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
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
6.45058	29.7446	22.9557

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
C1'	CD1	ILE- 21	4.13	0	Hydrophobic	false
C4'	CD1	ILE- 21	3.64	0	Hydrophobic	false
C6	CB	PRO- 139	4.08	0	Hydrophobic	false
O1B	OG	SER- 277	2.68	174.69	H-Bond (Protein Donor)	false
O2B	N	SER- 277	3.34	142.66	H-Bond (Protein Donor)	false
C1'	CH2	TRP- 346	3.78	0	Hydrophobic	false
N3	O	ALA- 347	2.65	160.15	H-Bond (Ligand Donor)	false
O7'	N	ALA- 347	3	166.07	H-Bond (Protein Donor)	false
C2'	CB	GLN- 349	4.14	0	Hydrophobic	false
O2B	NE2	HIS- 364	2.85	154.77	H-Bond (Protein Donor)	false
O4	N	TRP- 367	2.78	148.12	H-Bond (Protein Donor)	false
O1A	N	ASN- 368	2.93	143.34	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 368	2.92	142.62	H-Bond (Protein Donor)	false
C3'	CB	ASN- 368	3.78	0	Hydrophobic	false
O2A	N	SER- 369	2.92	138.45	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 372	2.66	146.35	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 372	2.62	150.22	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 372	3.23	145.28	H-Bond (Ligand Donor)	false
C2	CE1	TYR- 386	4.44	0	Hydrophobic	false
F1	CZ	TYR- 386	3.63	0	Hydrophobic	false
F1	CB	ALA- 387	4.01	0	Hydrophobic	false
O3	OE1	GLU- 388	2.7	154	H-Bond (Ligand Donor)	false
O4	OE2	GLU- 388	2.5	177.49	H-Bond (Ligand Donor)	false
O3	NE2	GLN- 389	2.92	169.29	H-Bond (Protein Donor)	false