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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4gtp

2.750 Å

X-ray

2012-08-29

Interactomes:
Molecular Function:
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
A6 %
B94 %


Ligand binding site composition:

B-Factor:35.694
Number of residues:31
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.563681.750

% Hydrophobic% Polar
43.5656.44
According to VolSite

Ligand :
4gtp_1 Structure
HET Code: 7TP
Formula: C33H32N4O6S
Molecular weight: 612.695 g/mol
DrugBank ID: -
Buried Surface Area:47.52 %
Polar Surface area: 126.49 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 6
Aromatic rings: 5
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 9

Mass center Coordinates

XYZ
51.310451.7714-4.18725


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CAQCD2LEU- 964.020Hydrophobic
CAXCH2TRP- 1063.860Hydrophobic
CAHCDARG- 2024.070Hydrophobic
CAXCD1TYR- 3613.710Hydrophobic
CAZCZTYR- 3613.960Hydrophobic
CAWCE1TYR- 3613.840Hydrophobic
CAVCBTYR- 3613.440Hydrophobic
NBAZN ZN- 5011.980Metal Acceptor
DuArZN ZN- 5013.1188.84Pi/Cation