2F0Y | pdb_00002f0y

Crystal Structure Of Human Protein Farnesyltransferase Complexed With Farnesyl Diphosphate and hydantoin derivative

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.258 (Depositor) 
  • R-Value Work: 
    0.212 (Depositor) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2F0Y

This is version 1.3 of the entry. See complete history. 

Literature

hydantoin derivatives as Non-pepridic inhibitors of Ras Farnesyl transferase

Lee, J., Kim, J., Koh, J.S., Chung, H.H., Ro, S., Kim, K.H.

To be published.

Macromolecule Content 

  • Total Structure Weight: 94.19 kDa 
  • Atom Count: 6,252 
  • Modeled Residue Count: 709 
  • Deposited Residue Count: 816 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit379Homo sapiensMutation(s): 0 
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49354 (Homo sapiens)
Explore P49354 
Go to UniProtKB:  P49354
PHAROS:  P49354
GTEx:  ENSG00000168522 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49354
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein farnesyltransferase beta subunit437Homo sapiensMutation(s): 0 
EC: 2.5.1.58
UniProt & NIH Common Fund Data Resources
Find proteins for P49356 (Homo sapiens)
Explore P49356 
Go to UniProtKB:  P49356
PHAROS:  P49356
GTEx:  ENSG00000257365 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49356
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3MN

Query on 3MN


Download:Ideal Coordinates CCD File
E [auth B]3-({3-[3-(1H-IMIDAZOL-1-YL)PROPYL]-5-METHYL-5-(1-NAPHTHYL)-2,4-DIOXOIMIDAZOLIDIN-1-YL}METHYL)BENZONITRILE
C28 H25 N5 O2
QRBLNORQTYKILD-MUUNZHRXSA-N
FPP

Query on FPP


Download:Ideal Coordinates CCD File
D [auth B]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3MN BindingDB:  2F0Y IC50: 0.09 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.258 (Depositor) 
  • R-Value Work:  0.212 (Depositor) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.888α = 90
b = 171.888β = 90
c = 71.367γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations