scPDB - 3ksl entry

Protein Data Bank Entry:

PDB ID : 3ksl

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2009-11-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein farnesyltransferase subunit beta
ID:	FNTB_RAT
AC:	Q02293
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.5.1.58

Chains:

Chain Name:	Percentage of Residues within binding site
A	23 %
B	77 %

Ligand binding site composition:

B-Factor:	26.480
Number of residues:	39
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.764	702.000

% Hydrophobic	% Polar
43.27	56.73
According to VolSite

Ligand :

HET Code:	SZH
Formula:	C13H22F3N2O9P2
Molecular weight:	469.265 g/mol
DrugBank ID:	-
Buried Surface Area:	54.99 %
Polar Surface area:	205.74 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
189.914	122.656	32.4302

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
F27	CZ2	TRP- 102	3.93	0	Hydrophobic	false
F26	CH2	TRP- 102	3.86	0	Hydrophobic	false
F26	CE2	TYR- 154	3.74	0	Hydrophobic	false
O18	NZ	LYS- 164	3.73	0	Ionic (Protein Cationic)	false
O21	NZ	LYS- 164	2.88	0	Ionic (Protein Cationic)	false
O21	NZ	LYS- 164	2.88	166.56	H-Bond (Protein Donor)	false
C5	CD2	TYR- 200	3.43	0	Hydrophobic	false
C7	CB	TYR- 200	4.32	0	Hydrophobic	false
C11	CD	ARG- 202	4.01	0	Hydrophobic	false
F27	CB	ARG- 202	4.22	0	Hydrophobic	false
F25	CD2	TYR- 205	3.46	0	Hydrophobic	false
F26	CE2	TYR- 205	4.29	0	Hydrophobic	false
F27	SG	CYS- 206	3.67	0	Hydrophobic	false
O20	NE2	HIS- 248	2.94	142.32	H-Bond (Protein Donor)	false
C5	CE1	TYR- 251	4.12	0	Hydrophobic	false
C9	CE1	TYR- 251	3.65	0	Hydrophobic	false
C13	SG	CYS- 254	4.04	0	Hydrophobic	false
O18	CZ	ARG- 291	3.96	0	Ionic (Protein Cationic)	false
O20	CZ	ARG- 291	3.39	0	Ionic (Protein Cationic)	false
O18	NH2	ARG- 291	2.75	132.28	H-Bond (Protein Donor)	false
O20	NE	ARG- 291	2.71	167.42	H-Bond (Protein Donor)	false
O20	NH2	ARG- 291	3.22	132.8	H-Bond (Protein Donor)	false
O17	NZ	LYS- 294	2.67	129.77	H-Bond (Protein Donor)	false
O18	NZ	LYS- 294	3.1	123.44	H-Bond (Protein Donor)	false
O17	NZ	LYS- 294	2.67	0	Ionic (Protein Cationic)	false
O18	NZ	LYS- 294	3.1	0	Ionic (Protein Cationic)	false
O16	OH	TYR- 300	2.62	154.87	H-Bond (Protein Donor)	false
C6	CE2	TRP- 303	3.99	0	Hydrophobic	false
F26	CH2	TRP- 303	3.62	0	Hydrophobic	false
O18	O	HOH- 465	3.05	137.31	H-Bond (Protein Donor)	false
O16	O	HOH- 474	2.87	154.37	H-Bond (Protein Donor)	false
N15	O	HOH- 545	3.34	122.93	H-Bond (Protein Donor)	false