scPDB - 4y38 entry

Protein Data Bank Entry:

PDB ID : 4y38

Resolution :1.100 Å

Experimental Method : X-ray

Deposition Date : 2015-02-10

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:	10.447
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.378	556.875

% Hydrophobic	% Polar
41.21	58.79
According to VolSite

Ligand :

HET Code:	0A9
Formula:	C10H14NO2
Molecular weight:	180.224 g/mol
DrugBank ID:	DB06838
Buried Surface Area:	58.33 %
Polar Surface area:	53.94 Å2

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

Mass center Coordinates

X	Y	Z
-1.03338	3.81777	9.64269

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
N	OD2	ASP- 35	3.17	158.49	H-Bond (Ligand Donor)	false
N	OD1	ASP- 35	2.8	133.43	H-Bond (Ligand Donor)	false
N	OD2	ASP- 35	3.17	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 35	2.8	0	Ionic (Ligand Cationic)	false
CB	CD1	TYR- 79	3.55	0	Hydrophobic	false
CD2	CB	TYR- 79	3.54	0	Hydrophobic	false
CM	CB	ASP- 81	4.24	0	Hydrophobic	false
CD1	CD2	LEU- 125	3.9	0	Hydrophobic	false
N	OD1	ASP- 219	3.06	149.47	H-Bond (Ligand Donor)	false
N	OD2	ASP- 219	2.92	141.54	H-Bond (Ligand Donor)	false
N	OD1	ASP- 219	3.06	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 219	2.92	0	Ionic (Ligand Cationic)	false
CM	CB	THR- 222	4.44	0	Hydrophobic	false