scPDB - 2wca entry

Protein Data Bank Entry:

PDB ID : 2wca

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-03-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	O-GlcNAcase BT_4395
ID:	OGA_BACTN
AC:	Q89ZI2
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.375
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.049	509.625

% Hydrophobic	% Polar
38.41	61.59
According to VolSite

Ligand :

HET Code:	NP6
Formula:	C17H23N3O7
Molecular weight:	381.380 g/mol
DrugBank ID:	DB07432
Buried Surface Area:	51.66 %
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:	7

Mass center Coordinates

X	Y	Z
-5.87967	-11.2997	7.81393

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
O2	O	GLY- 135	2.57	160.07	H-Bond (Ligand Donor)	false
C6	CE2	TYR- 137	4.36	0	Hydrophobic	false
C7	CD2	TYR- 137	4.28	0	Hydrophobic	false
C2	SG	CYS- 278	3.36	0	Hydrophobic	false
C2	CG	TYR- 282	3.83	0	Hydrophobic	false
C1	CD1	TYR- 282	3.92	0	Hydrophobic	false
C3	CZ	TYR- 282	3.6	0	Hydrophobic	false
C17	CH2	TRP- 286	3.28	0	Hydrophobic	false
C1	CG2	THR- 310	3.46	0	Hydrophobic	false
C9	CD1	ILE- 315	4	0	Hydrophobic	false
C2	CE3	TRP- 337	3.65	0	Hydrophobic	false
C1	CE2	TRP- 337	3.42	0	Hydrophobic	false
C3	CZ2	TRP- 337	4.14	0	Hydrophobic	false
O1	ND2	ASN- 339	3.06	160.04	H-Bond (Protein Donor)	false
C9	CG1	VAL- 342	3.99	0	Hydrophobic	false
O3	OD2	ASP- 344	2.57	153.96	H-Bond (Ligand Donor)	false
C9	CD1	TYR- 345	3.83	0	Hydrophobic	false
O3	ND2	ASN- 372	3.08	136.1	H-Bond (Protein Donor)	false
O7	NE2	HIS- 433	2.99	153.69	H-Bond (Protein Donor)	false