1LD7

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

• PDB DOI:  https://doi.org/10.2210/pdb1LD7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-04-08 Released: 2002-06-19 
• Deposition Author(s): Taylor, J.S., Terry, K.L., Beese, L.S.

---

Experimental Data Snapshot

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

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

• PubMed: 12036349 
• 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.93 kDa 
• Atom Count: 6,479 
• Modelled Residue Count: 720 
• Deposited Residue Count: 819 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein farnesyltransferase alpha subunit	A	382	Homo sapiens	Mutation(s): 0  Gene Names: FNTA 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
protein farnesyltransferase beta subunit	B	437	Homo sapiens	Mutation(s): 0  Gene Names: FNTB 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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U66	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	E [auth B]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FPP	BindingDB:  1LD7	Kd: 2 (nM) from 1 assay(s)
U66	Binding MOAD:  1LD7	IC50: 1.1 (nM) from 1 assay(s)
	PDBBind:  1LD7	IC50: 1.1 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Ligand Interaction

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 = 178.725	α = 90
b = 178.725	β = 90
c = 64.549	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-19 
Deposition Author(s): Taylor, J.S., Terry, K.L., Beese, L.S.

Revision History  

• 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