scPDB - 4gtm entry

Protein Data Bank Entry:

PDB ID : 4gtm

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-08-28

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	10 %
B	90 %

Ligand binding site composition:

B-Factor:	26.223
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.366	691.875

% Hydrophobic	% Polar
37.56	62.44
According to VolSite

Ligand :

HET Code:	7TM
Formula:	C36H42N6O5S
Molecular weight:	670.821 g/mol
DrugBank ID:	-
Buried Surface Area:	50.75 %
Polar Surface area:	138.16 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
52.8439	-52.3177	2.79423

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
CAO	SG	CYS- 95	4.17	0	Hydrophobic	false
CAQ	CD2	LEU- 96	3.94	0	Hydrophobic	false
CBJ	CD1	LEU- 96	4.33	0	Hydrophobic	false
CAV	CB	SER- 99	3.71	0	Hydrophobic	false
CAA	CB	PRO- 101	4.4	0	Hydrophobic	false
CAA	CB	TRP- 102	4.06	0	Hydrophobic	false
OAE	NE1	TRP- 102	2.93	131.26	H-Bond (Protein Donor)	false
CBB	CH2	TRP- 106	4.09	0	Hydrophobic	false
CAX	CE2	TYR- 131	4.29	0	Hydrophobic	false
CAY	CB	ALA- 151	3.66	0	Hydrophobic	false
CAV	CG	PRO- 152	3.3	0	Hydrophobic	false
CAM	CD	ARG- 202	4.34	0	Hydrophobic	false
CAI	CB	ASP- 359	4.41	0	Hydrophobic	false
CBA	CE1	TYR- 361	4.21	0	Hydrophobic	false
CBD	CZ	TYR- 361	4.29	0	Hydrophobic	false
CBB	CD1	TYR- 361	3.89	0	Hydrophobic	false
CAU	CB	TYR- 361	3.34	0	Hydrophobic	false
NBE	ZN	ZN- 501	2.14	0	Metal Acceptor	false
DuAr	ZN	ZN- 501	3.25	84.11	Pi/Cation	false