1LD8 | pdb_00001ld8

Co-crystal structure of Human Farnesyltransferase with farnesyldiphosphate and inhibitor compound 49


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.186 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

3-Aminopyrrolidinone farnesyltransferase inhibitors: design of macrocyclic compounds with improved pharmacokinetics and excellent cell potency.

Bell, I.M.Gallicchio, S.N.Abrams, M.Beese, L.S.Beshore, D.C.Bhimnathwala, H.Bogusky, M.J.Buser, C.A.Culberson, J.C.Davide, J.Ellis-Hutchings, M.Fernandes, C.Gibbs, J.B.Graham, S.L.Hamilton, K.A.Hartman, G.D.Heimbrook, D.C.Homnick, C.F.Huber, H.E.Huff, J.R.Kassahun, K.Koblan, K.S.Kohl, N.E.Lobell, R.B.Lynch Jr., J.J.Robinson, R.Rodrigues, A.D.Taylor, J.S.Walsh, E.S.Williams, T.M.Zartman, C.B.

(2002) J Med Chem 45: 2388-2409

  • DOI: https://doi.org/10.1021/jm010531d
  • Primary Citation Related Structures: 
    1LD7, 1LD8

  • PubMed Abstract: 

    A series of macrocyclic 3-aminopyrrolidinone farnesyltransferase inhibitors (FTIs) has been synthesized. Compared with previously described linear 3-aminopyrrolidinone FTIs such as compound 1, macrocycles such as 49 combined improved pharmacokinetic properties with a reduced potential for side effects. In dogs, oral bioavailability was good to excellent, and increases in plasma half-life were due to attenuated clearance. It was observed that in vivo clearance correlated with the flexibility of the molecules and this concept proved useful in the design of FTIs that exhibited low clearance, such as FTI 78. X-ray crystal structures of compounds 49 and 66 complexed with farnesyltransferase (FTase)-farnesyl diphosphate (FPP) were determined, and they provide details of the key interactions in such ternary complexes. Optimization of this 3-aminopyrrolidinone series of compounds led to significant increases in potency, providing 83 and 85, the most potent inhibitors of FTase in cells described to date.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. ian_bell@merck.com

Macromolecule Content 

  • Total Structure Weight: 95.03 kDa 
  • Atom Count: 6,657 
  • Modeled Residue Count: 720 
  • Deposited Residue Count: 819 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
protein farnesyltransferase alpha subunit382Homo sapiensMutation(s): 0 
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
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 (PDB Primary Data), 2.5.1.58 (UniProt)
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

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan: G05551OP
GlyCosmos: G05551OP

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U49

Query on U49



Download:Ideal Coordinates CCD File
H [auth B](20S)-19,20,21,22-TETRAHYDRO-19-OXO-5H-18,20-ETHANO-12,14-ETHENO-6,10-METHENO-18H-BENZ[D]IMIDAZO[4,3-K][1,6,9,12]OXATRI AZA-CYCLOOCTADECOSINE-9-CARBONITRILE
C26 H21 N5 O2
USPFJPDEADLGIG-HSZRJFAPSA-N
FPP

Query on FPP



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

Query on ZN



Download:Ideal Coordinates CCD File
F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY

Query on ACY



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.134α = 90
b = 178.134β = 90
c = 64.461γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary