scPDB - 3eq9 entry

Protein Data Bank Entry:

PDB ID : 3eq9

Resolution :2.470 Å

Experimental Method : X-ray

Deposition Date : 2008-09-30

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:	19.425
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.465	475.875

% Hydrophobic	% Polar
43.26	56.74
According to VolSite

Ligand :

HET Code:	X97
Formula:	C28H32N4O4
Molecular weight:	488.578 g/mol
DrugBank ID:	-
Buried Surface Area:	58.95 %
Polar Surface area:	90.03 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
7.52647	37.0841	32.8212

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	CE2	PHE- 173	3.81	0	Hydrophobic	false
C19	CB	MET- 235	3.65	0	Hydrophobic	false
C18	CB	ARG- 252	3.67	0	Hydrophobic	false
C12	CD	ARG- 252	3.62	0	Hydrophobic	false
C19	CG	ARG- 252	3.64	0	Hydrophobic	false
C21	CD	ARG- 252	4.05	0	Hydrophobic	false
N6	O	GLY- 254	3.21	135.75	H-Bond (Ligand Donor)	false
C1	SG	CYS- 255	4	0	Hydrophobic	false
CB	CG	PHE- 476	3.99	0	Hydrophobic	false
CB1	CE1	PHE- 476	3.58	0	Hydrophobic	false
CB1	CB	ASN- 555	3.94	0	Hydrophobic	false
CG1	CG2	VAL- 580	3.83	0	Hydrophobic	false
C2	CG1	ILE- 591	3.84	0	Hydrophobic	false
O	NE1	TRP- 595	2.59	148.12	H-Bond (Protein Donor)	false
CB1	CD2	TRP- 595	4.04	0	Hydrophobic	false
CG1	CZ2	TRP- 595	3.57	0	Hydrophobic	false
O1	NH1	ARG- 643	2.8	154.64	H-Bond (Protein Donor)	false
CG1	CG2	VAL- 644	3.41	0	Hydrophobic	false