scPDB - 2wb5 entry

Protein Data Bank Entry:

PDB ID : 2wb5

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2009-02-20

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	29 %
B	71 %

Ligand binding site composition:

B-Factor:	28.249
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.129	1242.000

% Hydrophobic	% Polar
38.32	61.68
According to VolSite

Ligand :

HET Code:	VGB
Formula:	C19H26N3O4
Molecular weight:	360.427 g/mol
DrugBank ID:	-
Buried Surface Area:	76.93 %
Polar Surface area:	109.46 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
2.65196	3.54327	17.4707

Binding mode :

What is Poseview ?

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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	2.58	151.91	H-Bond (Ligand Donor)	false
CAB	CE1	TYR- 189	4.07	0	Hydrophobic	false
CAA	CD1	TYR- 189	3.96	0	Hydrophobic	false
OAG	NZ	LYS- 218	3.14	135	H-Bond (Protein Donor)	false
CAN	CB	ASP- 297	3.69	0	Hydrophobic	false
NAK	OD2	ASP- 297	2.89	171.26	H-Bond (Ligand Donor)	false
CBA	CG2	VAL- 331	4.11	0	Hydrophobic	false
CBA	CD2	TYR- 335	3.69	0	Hydrophobic	false
CAN	CE2	TYR- 335	3.99	0	Hydrophobic	false
CAR	CG1	VAL- 370	3.52	0	Hydrophobic	false
CBA	CD2	TRP- 394	3.49	0	Hydrophobic	false
CAN	CE2	TRP- 394	3.93	0	Hydrophobic	false
CAB	CZ2	TRP- 394	4.2	0	Hydrophobic	false
OAM	ND2	ASN- 396	2.97	157.15	H-Bond (Protein Donor)	false
CAI	CG1	VAL- 399	4.35	0	Hydrophobic	false
OAH	OD2	ASP- 401	2.6	164.32	H-Bond (Ligand Donor)	false
OAJ	OD1	ASP- 401	2.67	165.27	H-Bond (Ligand Donor)	false
CAI	CD2	TYR- 402	4.02	0	Hydrophobic	false
CAR	CH2	TRP- 490	3.87	0	Hydrophobic	false
DuAr	NZ	LYS- 515	3.79	14.13	Pi/Cation	false
CAV	CD1	LEU- 621	3.53	0	Hydrophobic	false
CAW	CB	LEU- 623	3.92	0	Hydrophobic	false