scPDB - 2igx entry

Protein Data Bank Entry:

PDB ID : 2igx

Resolution :1.700 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:	31.614
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.401	374.625

% Hydrophobic	% Polar
69.37	30.63
According to VolSite

Ligand :

HET Code:	A1T
Formula:	C41H50N5O2
Molecular weight:	644.868 g/mol
DrugBank ID:	-
Buried Surface Area:	55.95 %
Polar Surface area:	70.84 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
58.8082	61.7897	8.95713

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
C9	CE1	PHE- 11	4.2	0	Hydrophobic	false
C12	CE	MET- 15	4.23	0	Hydrophobic	false
C8	CB	MET- 15	3.95	0	Hydrophobic	false
O1	OH	TYR- 17	3.14	121.62	H-Bond (Protein Donor)	false
C17	CG2	ILE- 32	3.91	0	Hydrophobic	false
C27	CB	SER- 37	4.22	0	Hydrophobic	false
C38	CD2	TRP- 41	3.9	0	Hydrophobic	false
C43	CB	TRP- 41	3.82	0	Hydrophobic	false
C48	CB	PRO- 43	4.34	0	Hydrophobic	false
C30	CE	MET- 75	3.96	0	Hydrophobic	false
C38	CG1	VAL- 82	4.26	0	Hydrophobic	false
C43	CG2	VAL- 105	4.3	0	Hydrophobic	false
C48	CG2	VAL- 105	4.34	0	Hydrophobic	false
C48	CG2	THR- 108	4.23	0	Hydrophobic	false
C38	CD2	PHE- 111	4.28	0	Hydrophobic	false
C40	CE2	PHE- 111	3.66	0	Hydrophobic	false
C43	CD2	PHE- 111	4.19	0	Hydrophobic	false
C10	CG2	THR- 114	3.9	0	Hydrophobic	false
C11	CG2	THR- 114	3.48	0	Hydrophobic	false
C46	CE2	TYR- 115	3.93	0	Hydrophobic	false
C48	CZ	TYR- 115	3.58	0	Hydrophobic	false
C13	CB	ALA- 117	4.04	0	Hydrophobic	false
C10	CB	SER- 118	4.33	0	Hydrophobic	false
C9	CB	SER- 118	4.42	0	Hydrophobic	false
C36	CD1	ILE- 123	3.84	0	Hydrophobic	false
C40	CD1	ILE- 123	3.63	0	Hydrophobic	false
C20	CD1	ILE- 123	3.94	0	Hydrophobic	false
C45	CZ	TYR- 192	3.21	0	Hydrophobic	false
C45	CD1	ILE- 212	3.79	0	Hydrophobic	false
N35	OD2	ASP- 214	3.78	0	Ionic (Ligand Cationic)	false
C47	CE1	PHE- 294	3.32	0	Hydrophobic	false
C42	CD1	ILE- 300	4.18	0	Hydrophobic	false
N35	O	HOH- 375	2.93	162.33	H-Bond (Ligand Donor)	false