scPDB - 4k10 entry

Protein Data Bank Entry:

PDB ID : 4k10

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-04-04

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
ID:	Q4QBL1_LEIMA
AC:	Q4QBL1
Organism:	Leishmania major
Reign:	Eukaryota
TaxID:	5664
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	96 %
D	4 %

Ligand binding site composition:

B-Factor:	39.591
Number of residues:	26
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.383	2180.250

% Hydrophobic	% Polar
34.21	65.79
According to VolSite

Ligand :

HET Code:	NI9
Formula:	C7H7FNO7P2
Molecular weight:	298.079 g/mol
DrugBank ID:	-
Buried Surface Area:	52.52 %
Polar Surface area:	170.11 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
27.9827	69.4486	129.639

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
F	CD2	PHE- 94	3.41	0	Hydrophobic	false
C7	CB	PHE- 94	3.87	0	Hydrophobic	false
C6	CD2	LEU- 95	4.14	0	Hydrophobic	false
O3	NH2	ARG- 107	2.83	165.91	H-Bond (Protein Donor)	false
O3	CZ	ARG- 107	3.81	0	Ionic (Protein Cationic)	false
F	CG2	THR- 163	4.18	0	Hydrophobic	false
C4	CG2	THR- 163	4.42	0	Hydrophobic	false
F	CG	GLN- 167	4.28	0	Hydrophobic	false
O4	NZ	LYS- 207	3.79	0	Ionic (Protein Cationic)	false
O6	NZ	LYS- 207	2.83	0	Ionic (Protein Cationic)	false
O6	NZ	LYS- 207	2.83	172.2	H-Bond (Protein Donor)	false
F	CG	LYS- 207	4.17	0	Hydrophobic	false
O4	MG	MG- 404	2.53	0	Metal Acceptor	false