scPDB - 4azh entry

Protein Data Bank Entry:

PDB ID : 4azh

Resolution :2.220 Å

Experimental Method : X-ray

Deposition Date : 2012-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-N-acetylhexosaminidase
ID:	STRH_STRPN
AC:	P49610
Organism:	Streptococcus pneumoniae serotype 4
Reign:	Bacteria
TaxID:	170187
EC Number:	3.2.1.52

Chains:

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

Ligand binding site composition:

B-Factor:	12.783
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.024	428.625

% Hydrophobic	% Polar
40.94	59.06
According to VolSite

Ligand :

HET Code:	LOG
Formula:	C8H14N2O6
Molecular weight:	234.207 g/mol
DrugBank ID:	-
Buried Surface Area:	69.43 %
Polar Surface area:	131.61 Å2

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

Mass center Coordinates

X	Y	Z
-43.573	-35.5911	-10.6743

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
O3	NH1	ARG- 641	3.26	135.94	H-Bond (Protein Donor)	false
O3	NH2	ARG- 641	2.96	149.93	H-Bond (Protein Donor)	false
O4	NH1	ARG- 641	2.9	129.86	H-Bond (Protein Donor)	false
C8	CB	ASP- 804	4.19	0	Hydrophobic	false
N2	OD2	ASP- 804	2.9	156.35	H-Bond (Ligand Donor)	false
C8	CG	PHE- 849	3.68	0	Hydrophobic	false
C8	CE2	TRP- 872	4.27	0	Hydrophobic	false
C5	CE2	TYR- 902	3.84	0	Hydrophobic	false
C6	CD2	TYR- 902	3.98	0	Hydrophobic	false
O7	OH	TYR- 902	2.63	127.9	H-Bond (Protein Donor)	false
C6	CD1	ILE- 904	3.64	0	Hydrophobic	false
C3	CZ3	TRP- 951	3.79	0	Hydrophobic	false
C6	CB	TRP- 951	4.04	0	Hydrophobic	false
C8	CH2	TRP- 951	4.19	0	Hydrophobic	false
C5	CD2	TRP- 951	3.85	0	Hydrophobic	false
O4	OD1	ASP- 953	2.74	153.33	H-Bond (Ligand Donor)	false
O4	OD2	ASP- 953	3.49	146.71	H-Bond (Ligand Donor)	false
O6	OD2	ASP- 953	2.73	170.66	H-Bond (Ligand Donor)	false
O3	O	HOH- 3038	2.55	155.74	H-Bond (Ligand Donor)	false