scPDB - 2cbj entry

Protein Data Bank Entry:

PDB ID : 2cbj

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2006-01-05

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	31 %
B	69 %

Ligand binding site composition:

B-Factor:	40.293
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.707	536.625

% Hydrophobic	% Polar
45.91	54.09
According to VolSite

Ligand :

HET Code:	OAN
Formula:	C15H19N3O7
Molecular weight:	353.327 g/mol
DrugBank ID:	-
Buried Surface Area:	78.73 %
Polar Surface area:	149.71 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
2.74972	3.59368	18.3512

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
OAJ	O	GLY- 187	2.63	142.59	H-Bond (Ligand Donor)	false
CAC	CE1	TYR- 189	4.24	0	Hydrophobic	false
CAD	CD1	TYR- 189	4.17	0	Hydrophobic	false
OAJ	NZ	LYS- 218	3.19	147.91	H-Bond (Protein Donor)	false
CAH	CB	ASP- 297	3.78	0	Hydrophobic	false
NAI	OD2	ASP- 297	2.82	173.1	H-Bond (Ligand Donor)	false
NAY	OD2	ASP- 298	2.88	157.1	H-Bond (Protein Donor)	false
CAH	CG2	VAL- 331	4.42	0	Hydrophobic	false
CAH	CE2	TYR- 335	3.79	0	Hydrophobic	false
OAQ	OH	TYR- 335	2.86	125.58	H-Bond (Protein Donor)	false
CAH	CG2	THR- 366	4.09	0	Hydrophobic	false
CAE	CG1	VAL- 370	4.08	0	Hydrophobic	false
CAF	CG2	VAL- 371	4.3	0	Hydrophobic	false
CAH	CE2	TRP- 394	3.58	0	Hydrophobic	false
CAC	CZ2	TRP- 394	4.18	0	Hydrophobic	false
OAN	ND2	ASN- 396	2.81	159.11	H-Bond (Protein Donor)	false
CAF	CG1	VAL- 399	4.4	0	Hydrophobic	false
OAK	OD2	ASP- 401	2.75	164.39	H-Bond (Ligand Donor)	false
CAF	CD2	TYR- 402	3.88	0	Hydrophobic	false
CAF	CH2	TRP- 490	4.34	0	Hydrophobic	false
CAT	CB	SER- 513	4.45	0	Hydrophobic	false
CAU	CG	LYS- 515	3.77	0	Hydrophobic	false
CAV	CD1	LEU- 621	3.7	0	Hydrophobic	false