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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:

3ksq

2.100 Å

X-ray

2009-11-23

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
A19 %
B81 %


Ligand binding site composition:

B-Factor:35.641
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.586901.125

% Hydrophobic% Polar
41.2058.80
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3ksqHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3ksq_1 Structure
HET Code: Z96
Formula: C28H33ClN5O3
Molecular weight: 523.046 g/mol
DrugBank ID: -
Buried Surface Area:50.21 %
Polar Surface area: 84.92 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
187.365129.55933.5458
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3ksqRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
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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
C22CZTYR- 934.330Hydrophobic
C26CE2TYR- 933.710Hydrophobic
C26SGCYS- 953.620Hydrophobic
C24SGCYS- 953.960Hydrophobic
C26CD1LEU- 963.820Hydrophobic
CLCBLYS- 1644.320Hydrophobic
CLCD1TYR- 16640Hydrophobic
C22CBASP- 3593.670Hydrophobic
C4CE1TYR- 3613.280Hydrophobic
N3ZN ZN- 20012.140Metal Acceptor
DuArZN ZN- 20013.2582.35Pi/Cation