scPDB - 3py4 entry

Protein Data Bank Entry:

PDB ID : 3py4

Resolution :2.420 Å

Experimental Method : X-ray

Deposition Date : 2010-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lactoperoxidase
ID:	PERL_BOVIN
AC:	P80025
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	1.11.1.7

Chains:

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

Ligand binding site composition:

B-Factor:	40.526
Number of residues:	18
Including
Standard Amino Acids:	16
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.468	931.500

% Hydrophobic	% Polar
43.12	56.88
According to VolSite

Ligand :

HET Code:	TYL
Formula:	C8H9NO2
Molecular weight:	151.163 g/mol
DrugBank ID:	DB00316
Buried Surface Area:	63.13 %
Polar Surface area:	49.33 Å2

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

Mass center Coordinates

X	Y	Z
4.008	3.85409	28.1485

Binding mode :

What is Poseview ?

2D View
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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
O4	NE2	HIS- 109	2.71	148.73	H-Bond (Protein Donor)	false
CM	CD2	PHE- 254	4.38	0	Hydrophobic	false
C6	CG	ARG- 255	3.64	0	Hydrophobic	false
CM	CB	ARG- 255	3.71	0	Hydrophobic	false
C2	CB	ARG- 255	3.92	0	Hydrophobic	false
C5	CD	ARG- 255	3.35	0	Hydrophobic	false
C3	CG	GLU- 258	3.38	0	Hydrophobic	false
CM	CB	GLU- 258	4.09	0	Hydrophobic	false
CM	CE1	PHE- 381	3.36	0	Hydrophobic	false