scPDB - 1xe5 entry

Protein Data Bank Entry:

PDB ID : 1xe5

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-09-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Plasmepsin-2
ID:	PLM2_PLAFA
AC:	P46925
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	5833
EC Number:	3.4.23.39

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
B	9 %

Ligand binding site composition:

B-Factor:	36.595
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.399	1238.625

% Hydrophobic	% Polar
45.23	54.77
According to VolSite

Ligand :

HET Code:	5FE
Formula:	C29H47F6N5O9
Molecular weight:	723.702 g/mol
DrugBank ID:	-
Buried Surface Area:	48.24 %
Polar Surface area:	212.25 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	7
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
60.6972	17.6378	9.62455

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
F1	CG2	ILE- 32	4.29	0	Hydrophobic	false
F1	CB	ASP- 34	4.45	0	Hydrophobic	false
O11	OD1	ASP- 34	2.73	169.09	H-Bond (Ligand Donor)	false
O11	OD2	ASP- 34	3.45	130.7	H-Bond (Ligand Donor)	false
N8	O	GLY- 36	3.01	144	H-Bond (Ligand Donor)	false
C29	CB	SER- 37	3.48	0	Hydrophobic	false
C29	CE	MET- 75	4.29	0	Hydrophobic	false
N5	O	ASN- 76	3.27	167.94	H-Bond (Ligand Donor)	false
F6	CB	ASN- 76	3.7	0	Hydrophobic	false
F2	CE1	TYR- 77	3.45	0	Hydrophobic	false
C13	CD1	TYR- 77	4.09	0	Hydrophobic	false
C33	CB	VAL- 78	4.13	0	Hydrophobic	false
C35	CG2	VAL- 78	3.84	0	Hydrophobic	false
F5	CG2	VAL- 78	3.41	0	Hydrophobic	false
O9	N	VAL- 78	3.34	159.81	H-Bond (Protein Donor)	false
N17	OG	SER- 79	3.15	149.11	H-Bond (Ligand Donor)	false
O15	OG	SER- 79	2.86	152.95	H-Bond (Protein Donor)	false
C37	CG2	THR- 114	3.99	0	Hydrophobic	false
F2	CD1	ILE- 123	3.87	0	Hydrophobic	false
C29	CG	LEU- 131	4.44	0	Hydrophobic	false
CA	CD1	ILE- 133	4.1	0	Hydrophobic	false
O6	OH	TYR- 192	2.6	152.65	H-Bond (Protein Donor)	false
O11	OD2	ASP- 214	2.77	161.89	H-Bond (Protein Donor)	false
N14	O	GLY- 216	3.37	131	H-Bond (Ligand Donor)	false
C34	CG2	THR- 217	3.67	0	Hydrophobic	false
N20	OG	SER- 218	3.1	135.33	H-Bond (Ligand Donor)	false
O18	N	SER- 218	2.97	152.56	H-Bond (Protein Donor)	false
C39	CB	ALA- 219	3.95	0	Hydrophobic	false
C24	CB	ALA- 219	4.27	0	Hydrophobic	false
C22	CB	PHE- 241	3.43	0	Hydrophobic	false
C24	CD2	LEU- 242	3.79	0	Hydrophobic	false
C24	CD1	ILE- 290	3.6	0	Hydrophobic	false
C39	CG1	ILE- 290	4.07	0	Hydrophobic	false
C35	CD1	ILE- 300	4.21	0	Hydrophobic	false