scPDB - 3pbz entry

Protein Data Bank Entry:

PDB ID : 3pbz

Resolution :1.480 Å

Experimental Method : X-ray

Deposition Date : 2010-10-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endothiapepsin
ID:	CARP_CRYPA
AC:	P11838
Organism:	Cryphonectria parasitica
Reign:	Eukaryota
TaxID:	5116
EC Number:	3.4.23.22

Chains:

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

Ligand binding site composition:

B-Factor:	15.029
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.648	715.500

% Hydrophobic	% Polar
43.87	56.13
According to VolSite

Ligand :

HET Code:	F02
Formula:	C11H17N3O
Molecular weight:	207.272 g/mol
DrugBank ID:	-
Buried Surface Area:	65.97 %
Polar Surface area:	58.36 Å2

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

Mass center Coordinates

X	Y	Z
-2.54913	1.24887	10.1701

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
C11	CB	ALA- 16	4.12	0	Hydrophobic	false
N15	OD1	ASP- 35	2.75	140.12	H-Bond (Ligand Donor)	false
C1	CB	TYR- 79	3.8	0	Hydrophobic	false
C8	CB	SER- 83	4.31	0	Hydrophobic	false
C9	CB	SER- 115	3.96	0	Hydrophobic	false
C8	CE1	PHE- 116	3.44	0	Hydrophobic	false
C9	CD1	PHE- 116	3.85	0	Hydrophobic	false
C10	CE1	PHE- 116	3.79	0	Hydrophobic	false
C11	CD1	ILE- 122	3.58	0	Hydrophobic	false
C3	CD2	LEU- 125	3.83	0	Hydrophobic	false
N15	OD2	ASP- 219	3.06	120.4	H-Bond (Ligand Donor)	false
N15	OD1	ASP- 219	3.07	150.72	H-Bond (Ligand Donor)	false