scPDB - 3ivm entry

Protein Data Bank Entry:

PDB ID : 3ivm

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2009-09-01

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:	Q9X6R4_AERCA
AC:	Q9X6R4
Organism:	Aeromonas caviae
Reign:	Bacteria
TaxID:	648
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.808
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.642	580.500

% Hydrophobic	% Polar
36.05	63.95
According to VolSite

Ligand :

HET Code:	ZPR
Formula:	C18H22N2O4
Molecular weight:	330.378 g/mol
DrugBank ID:	DB03535
Buried Surface Area:	50.55 %
Polar Surface area:	66.92 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
15.8612	93.6791	45.847

Binding mode :

What is Poseview ?

2D View
3D View

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
C5	CD1	ILE- 454	4.02	0	Hydrophobic	false
O17	OH	TYR- 456	3.32	141.42	H-Bond (Protein Donor)	false
C5	CE1	TYR- 483	4.09	0	Hydrophobic	false
O16	NE	ARG- 535	2.77	153.57	H-Bond (Protein Donor)	false
O16	NH2	ARG- 535	3.03	136.87	H-Bond (Protein Donor)	false
C4	CD	ARG- 535	4.21	0	Hydrophobic	false
C5	CG	ARG- 535	4.45	0	Hydrophobic	false
C22	CB	SER- 538	3.93	0	Hydrophobic	false
C18	CB	ALA- 561	4.39	0	Hydrophobic	false
C23	CG2	VAL- 562	3.62	0	Hydrophobic	false
O2	OG	SER- 670	2.5	153.53	H-Bond (Protein Donor)	false
C4	CG2	ILE- 673	4.08	0	Hydrophobic	false
C4	CE1	TYR- 674	3.74	0	Hydrophobic	false