scPDB - 3ez3 entry

Protein Data Bank Entry:

PDB ID : 3ez3

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-10-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Farnesyl pyrophosphate synthase, putative
ID:	A5K4U6_PLAVS
AC:	A5K4U6
Organism:	Plasmodium vivax
Reign:	Eukaryota
TaxID:	126793
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.463
Number of residues:	27
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.498	921.375

% Hydrophobic	% Polar
43.96	56.04
According to VolSite

Ligand :

HET Code:	IPE
Formula:	C5H9O7P2
Molecular weight:	243.068 g/mol
DrugBank ID:	DB04714
Buried Surface Area:	61.05 %
Polar Surface area:	141.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-23.6145	5.42414	21.8344

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
O1A	NZ	LYS- 81	2.51	136.56	H-Bond (Protein Donor)	false
O2B	N	LYS- 81	3.08	166.77	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 81	2.78	165.85	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 81	2.51	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 81	3.76	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 81	2.78	0	Ionic (Protein Cationic)	false
O1	NH2	ARG- 84	3.28	157.12	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 84	2.86	148.74	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 84	3.17	134.48	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 84	3.43	0	Ionic (Protein Cationic)	false
O1	NE2	GLN- 119	3.49	137.6	H-Bond (Protein Donor)	false
O3B	NE2	GLN- 119	3.06	154.17	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 136	3.74	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 136	3.58	0	Ionic (Protein Cationic)	false
O1B	NE	ARG- 136	3.02	137.87	H-Bond (Protein Donor)	false
C4	CG2	THR- 244	4.05	0	Hydrophobic	false
C4	CZ	TYR- 247	4.26	0	Hydrophobic	false
C2	CE2	PHE- 283	4.35	0	Hydrophobic	false
C4	CE2	PHE- 283	3.79	0	Hydrophobic	false
O3B	O	HOH- 1118	2.5	145.15	H-Bond (Protein Donor)	false