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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:

1mzc

2.000 Å

X-ray

2002-10-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protein farnesyltransferase subunit beta
ID:FNTB_HUMAN
AC:P49356
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.5.1.58


Chains:

Chain Name:Percentage of Residues
within binding site
A20 %
B80 %


Ligand binding site composition:

B-Factor:14.995
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.6581015.875

% Hydrophobic% Polar
35.5564.45
According to VolSite

Ligand :
1mzc_1 Structure
HET Code: BNE
Formula: C28H34N5O2
Molecular weight: 472.602 g/mol
DrugBank ID: -
Buried Surface Area:58.56 %
Polar Surface area: 98.79 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
17.1398133.836-2.6392


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
C5CD2LEU- 5963.80Hydrophobic
C4CBSER- 5994.070Hydrophobic
C13CZ3TRP- 6023.480Hydrophobic
C10CE2TRP- 6023.930Hydrophobic
C11CH2TRP- 6063.350Hydrophobic
C10CBALA- 6513.640Hydrophobic
N26NH1ARG- 7022.92127.92H-Bond
(Protein Donor)
C11CD1TYR- 8614.50Hydrophobic
NZZN ZN- 10011.930Metal Acceptor
DuArZN ZN- 10013.1183.52Pi/Cation