scPDB - 4bcd entry

Protein Data Bank Entry:

PDB ID : 4bcd

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-10-01

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:	11.410
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.632	556.875

% Hydrophobic	% Polar
39.39	60.61
According to VolSite

Ligand :

HET Code:	TDV
Formula:	C27H30FN5O2
Molecular weight:	475.558 g/mol
DrugBank ID:	-
Buried Surface Area:	49.44 %
Polar Surface area:	71.33 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
39.5671	37.5777	86.967

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	CE1	PHE- 173	3.89	0	Hydrophobic	false
C14	CD1	PHE- 173	3.46	0	Hydrophobic	false
C19	SD	MET- 235	3.85	0	Hydrophobic	false
C15	CE	MET- 235	3.93	0	Hydrophobic	false
C18	CB	ARG- 252	3.86	0	Hydrophobic	false
C19	SG	CYS- 255	4.34	0	Hydrophobic	false
C22	CB	PHE- 476	4.49	0	Hydrophobic	false
C23	CG	PHE- 476	4.06	0	Hydrophobic	false
C2	CE2	PHE- 476	3.66	0	Hydrophobic	false
C29	CD1	ILE- 478	3.95	0	Hydrophobic	false
C2	CB	ASN- 555	3.91	0	Hydrophobic	false
C3	CG2	VAL- 580	3.54	0	Hydrophobic	false
C20	CG1	ILE- 591	4.21	0	Hydrophobic	false
C13	CG1	ILE- 591	3.7	0	Hydrophobic	false
C20	CB	ALA- 594	3.75	0	Hydrophobic	false
C3	CZ2	TRP- 595	3.63	0	Hydrophobic	false
C2	CD2	TRP- 595	4.22	0	Hydrophobic	false
O11	NE1	TRP- 595	2.8	151.14	H-Bond (Protein Donor)	false
O7	NH1	ARG- 643	2.81	160.41	H-Bond (Protein Donor)	false
C3	CG2	VAL- 644	3.5	0	Hydrophobic	false