scPDB - 1xrp entry

Protein Data Bank Entry:

PDB ID : 1xrp

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2004-10-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proline iminopeptidase
ID:	PIP_THEAC
AC:	P96084
Organism:	Thermoplasma acidophilum
Reign:	Archaea
TaxID:	273075
EC Number:	3.4.11.5

Chains:

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

Ligand binding site composition:

B-Factor:	33.389
Number of residues:	22
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.673	418.500

% Hydrophobic	% Polar
45.16	54.84
According to VolSite

Ligand :

HET Code:	PRO_LEU_GLY_GLY
Formula:	C15H26N4O5
Molecular weight:	342.391 g/mol
DrugBank ID:	-
Buried Surface Area:	40.92 %
Polar Surface area:	144.03 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
7.91825	16.0604	16.9894

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
CD1	CG1	VAL- 174	4.04	0	Hydrophobic	false
CB	CZ	TYR- 178	4.02	0	Hydrophobic	false
CB	CE2	TYR- 178	3.85	0	Hydrophobic	false
CG	CD2	LEU- 196	3.43	0	Hydrophobic	false
N	OE1	GLU- 200	3.74	0	Ionic (Ligand Cationic)	false
CB	CZ	TYR- 205	3.84	0	Hydrophobic	false
CB	CB	ASN- 212	4.47	0	Hydrophobic	false
CG	CG	GLN- 213	4.07	0	Hydrophobic	false