scPDB - 2igy entry

Protein Data Bank Entry:

PDB ID : 2igy

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2006-09-25

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:	Q17SC2_PLAFA
AC:	Q17SC2
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	5833
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	70.988
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.509	867.375

% Hydrophobic	% Polar
52.14	47.86
According to VolSite

Ligand :

HET Code:	A2T
Formula:	C35H50N4O
Molecular weight:	542.798 g/mol
DrugBank ID:	-
Buried Surface Area:	56.39 %
Polar Surface area:	42.13 Å2

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

Mass center Coordinates

X	Y	Z
42.818	-2.8925	-13.1324

Binding mode :

What is Poseview ?

2D View
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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
C8	CE	MET- 15	4.12	0	Hydrophobic	false
C12	CD1	ILE- 32	4.43	0	Hydrophobic	false
C45	CD1	ILE- 32	3.45	0	Hydrophobic	false
C13	CG2	ILE- 32	4.01	0	Hydrophobic	false
C24	CB	SER- 37	3.84	0	Hydrophobic	false
C35	CD2	TRP- 41	4.3	0	Hydrophobic	false
C31	CE2	TRP- 41	3.48	0	Hydrophobic	false
C39	CB	TRP- 41	3.61	0	Hydrophobic	false
C43	CB	PRO- 43	4.44	0	Hydrophobic	false
C33	CE	MET- 75	4.06	0	Hydrophobic	false
C35	CG1	VAL- 82	4.11	0	Hydrophobic	false
C39	CG2	VAL- 105	4.07	0	Hydrophobic	false
C43	CG2	VAL- 105	4.35	0	Hydrophobic	false
C35	CD2	PHE- 111	4.34	0	Hydrophobic	false
C37	CE2	PHE- 111	4.18	0	Hydrophobic	false
C45	CZ	PHE- 111	4.35	0	Hydrophobic	false
C30	CE1	PHE- 111	3.46	0	Hydrophobic	false
C45	CG2	THR- 114	4.12	0	Hydrophobic	false
C42	CE2	TYR- 115	4.05	0	Hydrophobic	false
C43	CZ	TYR- 115	4.24	0	Hydrophobic	false
C45	CZ	PHE- 120	3.9	0	Hydrophobic	false
C37	CD1	ILE- 123	3.83	0	Hydrophobic	false
C17	CD1	ILE- 123	3.73	0	Hydrophobic	false
C33	CD1	ILE- 123	3.97	0	Hydrophobic	false
C41	CD2	TYR- 192	3.72	0	Hydrophobic	false
C36	CE2	TYR- 192	3.69	0	Hydrophobic	false
C41	CG2	ILE- 212	3.38	0	Hydrophobic	false
C40	CD1	ILE- 212	4.44	0	Hydrophobic	false
C41	CB	ASP- 214	4.17	0	Hydrophobic	false
N6	OG	SER- 218	3.23	178.51	H-Bond (Protein Donor)	false
C40	CZ	PHE- 294	4.05	0	Hydrophobic	false
C38	CD1	ILE- 300	4.08	0	Hydrophobic	false
N32	O	HOH- 352	2.8	176.95	H-Bond (Ligand Donor)	false