scPDB - 2vs5 entry

Protein Data Bank Entry:

PDB ID : 2vs5

Resolution :1.820 Å

Experimental Method : X-ray

Deposition Date : 2008-04-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acetyllactosaminide alpha-1,3-galactosyltransferase
ID:	GGTA1_BOVIN
AC:	P14769
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.761
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.676	1029.375

% Hydrophobic	% Polar
43.28	56.72
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	71.81 %
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
5.17542	23.4667	23.1517

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
O2D	O	PHE- 134	2.56	156.87	H-Bond (Ligand Donor)	false
N3	O	VAL- 136	2.94	171.48	H-Bond (Ligand Donor)	false
O2	N	VAL- 136	2.83	156.4	H-Bond (Protein Donor)	false
C3D	CE1	TYR- 139	3.73	0	Hydrophobic	false
C2D	CD1	TYR- 139	3.66	0	Hydrophobic	false
O2A	OH	TYR- 139	2.73	146.83	H-Bond (Protein Donor)	false
C6'	CZ3	TRP- 195	4.34	0	Hydrophobic	false
C1D	CG2	ILE- 198	3.97	0	Hydrophobic	false
C5D	CB	SER- 199	4.15	0	Hydrophobic	false
C6'	CB	SER- 199	4.45	0	Hydrophobic	false
O3'	NH2	ARG- 202	2.87	144.8	H-Bond (Protein Donor)	false
C3D	CB	ASP- 225	4.48	0	Hydrophobic	false
O2'	OD2	ASP- 225	2.82	176.83	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 225	3.02	161.22	H-Bond (Ligand Donor)	false
O3D	N	VAL- 226	3	142.72	H-Bond (Protein Donor)	false
C2D	CG1	VAL- 226	3.65	0	Hydrophobic	false
O3D	OD1	ASP- 227	2.9	143.63	H-Bond (Ligand Donor)	false
C3'	CB	ALA- 281	3.97	0	Hydrophobic	false
C6'	CB	HIS- 315	3.85	0	Hydrophobic	false
O6'	ND1	HIS- 315	2.83	141.72	H-Bond (Protein Donor)	false
O4'	OD2	ASP- 316	2.79	135.27	H-Bond (Ligand Donor)	false
O2A	NH2	ARG- 365	3.03	154.79	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 365	3.92	0	Ionic (Protein Cationic)	false
O1A	MN	MN- 1366	2.38	0	Metal Acceptor	false
O2B	MN	MN- 1366	2.61	0	Metal Acceptor	false
O2D	O	HOH- 2205	2.85	179.97	H-Bond (Protein Donor)	false
O3'	O	HOH- 2302	3.27	129.89	H-Bond (Protein Donor)	false