scPDB - 3eq7 entry

Protein Data Bank Entry:

PDB ID : 3eq7

Resolution :2.890 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:	23.397
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.200	354.375

% Hydrophobic	% Polar
39.05	60.95
According to VolSite

Ligand :

HET Code:	X99
Formula:	C20H21F2N3O4
Molecular weight:	405.395 g/mol
DrugBank ID:	DB08739
Buried Surface Area:	54.51 %
Polar Surface area:	78 Å2

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

Mass center Coordinates

X	Y	Z
6.71297	38.2989	31.5074

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
C13	CB	PHE- 173	3.59	0	Hydrophobic	false
C12	CB	PHE- 173	3.5	0	Hydrophobic	false
C9	SD	MET- 235	4.34	0	Hydrophobic	false
CA	SG	CYS- 255	4.05	0	Hydrophobic	false
CA	CE2	PHE- 476	4.29	0	Hydrophobic	false
F1	CB	PHE- 476	3.76	0	Hydrophobic	false
CG1	CE1	PHE- 476	3.59	0	Hydrophobic	false
CB	CD2	PHE- 476	3.34	0	Hydrophobic	false
F1	CD1	ILE- 478	3.87	0	Hydrophobic	false
F2	CD1	ILE- 478	4.12	0	Hydrophobic	false
CB1	CB	SER- 554	4.36	0	Hydrophobic	false
CG1	CB	ASN- 555	4.02	0	Hydrophobic	false
CB1	CG2	VAL- 580	3.45	0	Hydrophobic	false
O	NE1	TRP- 595	2.7	152.61	H-Bond (Protein Donor)	false
CA	CE2	TRP- 595	4.2	0	Hydrophobic	false
CB1	CZ2	TRP- 595	4.05	0	Hydrophobic	false
CG1	CD2	TRP- 595	4.44	0	Hydrophobic	false
O1	NH1	ARG- 643	2.73	163.24	H-Bond (Protein Donor)	false
CB1	CG2	VAL- 644	4.17	0	Hydrophobic	false