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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:

3pz4

2.100 Å

X-ray

2010-12-14

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
A12 %
B88 %


Ligand binding site composition:

B-Factor:23.832
Number of residues:25
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.8341326.375

% Hydrophobic% Polar
39.6960.31
According to VolSite

Ligand :
3pz4_1 Structure
HET Code: 3PZ
Formula: C29H29N5O3S
Molecular weight: 527.637 g/mol
DrugBank ID: -
Buried Surface Area:47.41 %
Polar Surface area: 99.83 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 0
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
51.0665-50.99434.20639


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
N3ZN ZN- 12.130Metal Acceptor
DuArZN ZN- 13.2192.28Pi/Cation
C23SGCYS- 953.880Hydrophobic
C7CD2LEU- 964.490Hydrophobic
C24CD2LEU- 964.060Hydrophobic
C3CD1LEU- 964.040Hydrophobic
C7CH2TRP- 1063.960Hydrophobic
C7CD1TYR- 3614.140Hydrophobic
C9CZTYR- 3614.230Hydrophobic
C4CBTYR- 3613.20Hydrophobic