scPDB - 1me6 entry

Protein Data Bank Entry:

PDB ID : 1me6

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2002-08-08

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
B	100 %

Ligand binding site composition:

B-Factor:	28.273
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.331	668.250

% Hydrophobic	% Polar
54.55	45.45
According to VolSite

Ligand :

HET Code:	IVS
Formula:	C25H47N3O6
Molecular weight:	485.657 g/mol
DrugBank ID:	-
Buried Surface Area:	55.94 %
Polar Surface area:	133.82 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
15.8409	91.5741	58.7561

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
C63	CG2	ILE- 32	4.16	0	Hydrophobic	false
O72	OD1	ASP- 34	3.24	146.19	H-Bond (Ligand Donor)	false
O72	OD2	ASP- 34	3.23	157.22	H-Bond (Ligand Donor)	false
C76	CB	SER- 37	4.06	0	Hydrophobic	false
C76	CE	MET- 75	4.46	0	Hydrophobic	false
C52	CB	TYR- 77	4.2	0	Hydrophobic	false
C51	CD1	TYR- 77	3.89	0	Hydrophobic	false
C60	CD1	TYR- 77	4.1	0	Hydrophobic	false
C67	CB	TYR- 77	3.96	0	Hydrophobic	false
C76	CD1	TYR- 77	4.03	0	Hydrophobic	false
C52	CG2	VAL- 78	4.44	0	Hydrophobic	false
C40	CB	VAL- 78	3.65	0	Hydrophobic	false
O19	N	SER- 79	2.94	120.37	H-Bond (Protein Donor)	false
N19	OG	SER- 79	2.63	174.64	H-Bond (Ligand Donor)	false
C67	CB	SER- 79	3.78	0	Hydrophobic	false
C67	CZ	PHE- 111	3.87	0	Hydrophobic	false
C63	CZ	PHE- 111	4.38	0	Hydrophobic	false
C31	CG2	THR- 114	4.21	0	Hydrophobic	false
C63	CD1	ILE- 123	3.44	0	Hydrophobic	false
C57	CZ	TYR- 192	4.23	0	Hydrophobic	false
C44	CG2	THR- 217	4.09	0	Hydrophobic	false
O36	N	SER- 218	2.89	157.24	H-Bond (Protein Donor)	false
N16	OG	SER- 218	2.96	155.91	H-Bond (Ligand Donor)	false
C25	CB	SER- 218	4.48	0	Hydrophobic	false
C6	CB	ALA- 219	3.74	0	Hydrophobic	false
C1	CE1	PHE- 244	4.05	0	Hydrophobic	false
C6	CG1	ILE- 290	3.77	0	Hydrophobic	false
C40	CD2	LEU- 292	4	0	Hydrophobic	false
C40	CD1	ILE- 300	3.64	0	Hydrophobic	false