scPDB - 1e8m entry

Protein Data Bank Entry:

PDB ID : 1e8m

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2000-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prolyl endopeptidase
ID:	PPCE_PIG
AC:	P23687
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	3.4.21.26

Chains:

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

Ligand binding site composition:

B-Factor:	8.425
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.414	691.875

% Hydrophobic	% Polar
33.17	66.83
According to VolSite

Ligand :

HET Code:	P0H
Formula:	C15H17N2O5
Molecular weight:	305.306 g/mol
DrugBank ID:	-
Buried Surface Area:	65.06 %
Polar Surface area:	98.77 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
41.5115	37.5996	85.0055

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
C2	CE1	PHE- 173	3.84	0	Hydrophobic	false
C8	CB	PHE- 173	4.17	0	Hydrophobic	false
C6	SD	MET- 235	3.56	0	Hydrophobic	false
C7	CE	MET- 235	3.51	0	Hydrophobic	false
C4	SG	CYS- 255	4.08	0	Hydrophobic	false
O	OH	TYR- 473	2.66	147.89	H-Bond (Protein Donor)	false
CG	CE2	PHE- 476	3.48	0	Hydrophobic	false
CB	CB	ALA- 554	4.09	0	Hydrophobic	false
O	N	ASN- 555	3.02	155.24	H-Bond (Protein Donor)	false
CG	CB	ASN- 555	4.11	0	Hydrophobic	false
CB	CG2	VAL- 580	3.69	0	Hydrophobic	false
C4	CG1	ILE- 591	3.85	0	Hydrophobic	false
C4	CB	ALA- 594	3.68	0	Hydrophobic	false
O1	NE1	TRP- 595	2.92	163.67	H-Bond (Protein Donor)	false
CB	CZ2	TRP- 595	3.88	0	Hydrophobic	false
CG	CD2	TRP- 595	3.81	0	Hydrophobic	false
CG	CE2	TYR- 599	4.43	0	Hydrophobic	false
O3	NH1	ARG- 643	2.82	163.65	H-Bond (Protein Donor)	false
CB	CG2	VAL- 644	3.75	0	Hydrophobic	false
OXT	NE2	HIS- 680	2.77	168.03	H-Bond (Protein Donor)	false