scPDB - 2x0y entry

Protein Data Bank Entry:

PDB ID : 2x0y

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2009-12-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	O-GlcNAcase NagJ
ID:	OGA_CLOP1
AC:	Q0TR53
Organism:	Clostridium perfringens
Reign:	Bacteria
TaxID:	195103
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	20.551
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.516	475.875

% Hydrophobic	% Polar
51.77	48.23
According to VolSite

Ligand :

HET Code:	X0T
Formula:	C10H14N4O4
Molecular weight:	254.243 g/mol
DrugBank ID:	-
Buried Surface Area:	73.16 %
Polar Surface area:	98.9 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
2.08672	1.54561	15.0643

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
N9	NZ	LYS- 218	2.93	160.52	H-Bond (Protein Donor)	false
CAB	CD1	TYR- 295	4.41	0	Hydrophobic	false
CAA	CG1	VAL- 331	3.79	0	Hydrophobic	false
CAA	CD2	TYR- 335	3.4	0	Hydrophobic	false
CAA	CG2	THR- 366	3.59	0	Hydrophobic	false
CAI	CG1	VAL- 370	4.3	0	Hydrophobic	false
CAH	CG2	VAL- 371	4.24	0	Hydrophobic	false
CAB	CH2	TRP- 394	3.75	0	Hydrophobic	false
CAA	CD2	TRP- 394	3.66	0	Hydrophobic	false
O6	ND2	ASN- 396	2.98	172.97	H-Bond (Protein Donor)	false
OAF	OD2	ASP- 401	2.67	166.16	H-Bond (Ligand Donor)	false
OAE	OD1	ASP- 401	2.59	165.53	H-Bond (Ligand Donor)	false
CAH	CD2	TYR- 402	4.2	0	Hydrophobic	false