scPDB - 1lf2 entry

Protein Data Bank Entry:

PDB ID : 1lf2

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2002-04-10

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	100 %

Ligand binding site composition:

B-Factor:	15.901
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.291	786.375

% Hydrophobic	% Polar
49.79	50.21
According to VolSite

Ligand :

HET Code:	R37
Formula:	C32H41N3O4
Molecular weight:	531.686 g/mol
DrugBank ID:	DB04378
Buried Surface Area:	57.86 %
Polar Surface area:	113.68 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
31.9371	33.3756	12.3643

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
C24	CG2	ILE- 32	4.45	0	Hydrophobic	false
O14	OD1	ASP- 34	3.28	132.61	H-Bond (Ligand Donor)	false
N3	O	GLY- 36	3.14	133.29	H-Bond (Ligand Donor)	false
C26	CB	SER- 37	4.12	0	Hydrophobic	false
C18	CD2	TYR- 77	4.25	0	Hydrophobic	false
C20	CD2	TYR- 77	3.43	0	Hydrophobic	false
C20	CB	TYR- 77	3.9	0	Hydrophobic	false
C3	CG2	VAL- 78	4.22	0	Hydrophobic	false
C34	CG2	VAL- 78	3.77	0	Hydrophobic	false
C11	CG1	VAL- 78	3.84	0	Hydrophobic	false
O2	N	VAL- 78	3.09	133.63	H-Bond (Protein Donor)	false
C34	CB	SER- 79	4.12	0	Hydrophobic	false
C21	CB	SER- 79	3.55	0	Hydrophobic	false
O26	N	SER- 79	3.39	134.53	H-Bond (Protein Donor)	false
O26	OG	SER- 79	2.99	127.41	H-Bond (Protein Donor)	false
C21	CD1	ILE- 123	3.5	0	Hydrophobic	false
C27	CG	LEU- 131	3.94	0	Hydrophobic	false
N1	O	LEU- 131	2.91	144.4	H-Bond (Ligand Donor)	false
C7	CZ	TYR- 192	3.87	0	Hydrophobic	false
C5	CE2	TYR- 192	3.87	0	Hydrophobic	false
C7	CD1	ILE- 212	4.41	0	Hydrophobic	false
O14	OD1	ASP- 214	2.57	155.56	H-Bond (Protein Donor)	false
C9	CG2	THR- 217	3.61	0	Hydrophobic	false
C13	CB	ALA- 219	4.15	0	Hydrophobic	false
C10	CG2	THR- 221	4.05	0	Hydrophobic	false
C10	CD1	ILE- 290	3.88	0	Hydrophobic	false
C3	CD2	LEU- 292	4.41	0	Hydrophobic	false
C7	CE1	PHE- 294	3.59	0	Hydrophobic	false
C3	CD1	ILE- 300	4.11	0	Hydrophobic	false
C11	CD1	ILE- 300	3.97	0	Hydrophobic	false