scPDB - 3pgi entry

Protein Data Bank Entry:

PDB ID : 3pgi

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-11-02

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:	23.011
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.824	715.500

% Hydrophobic	% Polar
48.58	51.42
According to VolSite

Ligand :

HET Code:	F41
Formula:	C14H19N2O3
Molecular weight:	263.312 g/mol
DrugBank ID:	-
Buried Surface Area:	54.64 %
Polar Surface area:	52 Å2

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

Mass center Coordinates

X	Y	Z
-0.406263	6.08542	9.23332

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
C2	CG	TYR- 79	3.53	0	Hydrophobic	false
N4	OD2	ASP- 81	2.99	134.65	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 81	2.99	0	Ionic (Ligand Cationic)	false
O9	N	ASP- 81	2.88	125.8	H-Bond (Protein Donor)	false
C1	CE1	PHE- 116	3.88	0	Hydrophobic	false
C2	CZ	PHE- 116	4.14	0	Hydrophobic	false
C2	CD2	LEU- 125	3.73	0	Hydrophobic	false
C18	CZ	PHE- 194	4.15	0	Hydrophobic	false
C14	CD1	ILE- 217	4.05	0	Hydrophobic	false
C16	CB	THR- 222	4.38	0	Hydrophobic	false
C18	CG2	ILE- 302	3.75	0	Hydrophobic	false
C14	CD1	ILE- 304	3.7	0	Hydrophobic	false