scPDB - 2xpk entry

Protein Data Bank Entry:

PDB ID : 2xpk

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-08-26

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	72 %
B	28 %

Ligand binding site composition:

B-Factor:	30.209
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.244	843.750

% Hydrophobic	% Polar
50.40	49.60
According to VolSite

Ligand :

HET Code:	Z0M
Formula:	C19H26N3O4S
Molecular weight:	392.492 g/mol
DrugBank ID:	-
Buried Surface Area:	76.42 %
Polar Surface area:	147.66 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
2.64704	2.94596	17.5766

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
OAG	O	GLY- 187	2.55	154.93	H-Bond (Ligand Donor)	false
CAB	CE1	TYR- 189	4.2	0	Hydrophobic	false
CAA	CD1	TYR- 189	3.94	0	Hydrophobic	false
OAG	NZ	LYS- 218	2.93	159.31	H-Bond (Protein Donor)	false
CAN	CB	ASP- 297	3.7	0	Hydrophobic	false
NAK	OD2	ASP- 297	2.83	172.81	H-Bond (Ligand Donor)	false
SAZ	CB	CYS- 331	3.48	0	Hydrophobic	false
CAZ	CD2	TYR- 335	3.45	0	Hydrophobic	false
CAN	CZ	TYR- 335	4.01	0	Hydrophobic	false
SAZ	CB	TYR- 335	3.86	0	Hydrophobic	false
SAZ	CB	MET- 364	4.38	0	Hydrophobic	false
CAZ	CG2	THR- 366	3.27	0	Hydrophobic	false
CAR	CG1	VAL- 370	3.61	0	Hydrophobic	false
CAZ	CD2	TRP- 394	3.73	0	Hydrophobic	false
CAN	CE2	TRP- 394	3.85	0	Hydrophobic	false
CAB	CZ2	TRP- 394	4.09	0	Hydrophobic	false
SAZ	CE3	TRP- 394	3.79	0	Hydrophobic	false
OAM	ND2	ASN- 396	3	167.55	H-Bond (Protein Donor)	false
CAI	CG2	VAL- 399	4.43	0	Hydrophobic	false
OAH	OD2	ASP- 401	2.5	162.65	H-Bond (Ligand Donor)	false
OAJ	OD2	ASP- 401	3.4	127.64	H-Bond (Ligand Donor)	false
CAI	CD2	TYR- 402	3.98	0	Hydrophobic	false
OAH	ND2	ASN- 429	2.96	124.15	H-Bond (Protein Donor)	false
CAR	CH2	TRP- 490	3.96	0	Hydrophobic	false
CAT	CD	LYS- 515	4.15	0	Hydrophobic	false
CAX	CD2	LEU- 621	4.32	0	Hydrophobic	false
CAV	CB	LEU- 623	4.27	0	Hydrophobic	false