1LD7

Co-crystal structure of Human Farnesyltransferase with farnesyldiphosphate and inhibitor compound 66


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 

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 of 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
protein farnesyltransferase alpha subunit382Homo sapiensMutation(s): 0 
EC: 2.5.1
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
protein farnesyltransferase beta subunit437Homo sapiensMutation(s): 0 
EC: 2.5.1
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 Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U66
Query on U66

Download Ideal Coordinates CCD File 
F [auth B](20S)-19,20,22,23-TETRAHYDRO-19-OXO-5H,21H-18,20-ETHANO-12,14-ETHENO-6,10-METHENOBENZ[D]IMIDAZO[4,3-L][1,6,9,13]OXATRIA ZACYCLONOADECOSINE-9-CARBONITRILE
C27 H27 N5 O2
GBEQWWUQNVMGMR-LLHWJCAFSA-N
FPP
Query on FPP

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

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FPP BindingDB:  1LD7 Kd: 2 (nM) from 1 assay(s)
U66 PDBBind:  1LD7 IC50: 1.1 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.725α = 90
b = 178.725β = 90
c = 64.549γ = 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