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- PDB-1n94: Aryl Tetrahydropyridine Inhbitors of Farnesyltransferase: Glycine... -

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Basic information

Entry
Database: PDB / ID: 1n94
TitleAryl Tetrahydropyridine Inhbitors of Farnesyltransferase: Glycine, Phenylalanine and Histidine Derivates
Components
  • Protein farnesyltransferase alpha subunit
  • Protein farnesyltransferase beta subunit
KeywordsTRANSFERASE / Farnesyltransferase / Prenyltransferase
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / regulation of fibroblast proliferation / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / response to organic cyclic compound / receptor tyrosine kinase binding / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID / Chem-TIN / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsGwaltney II, S.L. / O'Connor, S.J. / Nelson, L.T. / Sullivan, G.M. / Imade, H. / Wang, W. / Hasvold, L. / Li, Q. / Cohen, J. / Gu, W.Z.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: Aryl tetrahydropyridine inhibitors of farnesyltransferase: glycine, phenylalanine and histidine derivatives.
Authors: Gwaltney II, S.L. / O'Connor, S.J. / Nelson, L.T. / Sullivan, G.M. / Imade, H. / Wang, W. / Hasvold, L. / Li, Q. / Cohen, J. / Gu, W.Z. / Tahir, S.K. / Bauch, J. / Marsh, K. / Ng, S.C. / ...Authors: Gwaltney II, S.L. / O'Connor, S.J. / Nelson, L.T. / Sullivan, G.M. / Imade, H. / Wang, W. / Hasvold, L. / Li, Q. / Cohen, J. / Gu, W.Z. / Tahir, S.K. / Bauch, J. / Marsh, K. / Ng, S.C. / Frost, D.J. / Zhang, H. / Muchmore, S. / Jakob, C.G. / Stoll, V. / Hutchins, C. / Rosenberg, S.H. / Sham, H.L.
History
DepositionNov 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein farnesyltransferase alpha subunit
B: Protein farnesyltransferase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4205
Polymers82,5082
Non-polymers9133
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-60 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.106, 172.106, 69.404
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein farnesyltransferase alpha subunit / CAAX farnesyl transferase alpha subunit / RAS proteins prenyltransferase alpha / FTase-alpha


Mass: 38028.766 Da / Num. of mol.: 1 / Fragment: residues 55-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein Protein farnesyltransferase beta subunit / CAAX farnesyl transferase beta subunit / RAS proteins prenyltransferase beta / FTase-beta


Mass: 44478.828 Da / Num. of mol.: 1 / Fragment: residues 22-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#3: Chemical ChemComp-HFP / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID


Mass: 308.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H33O4P
#4: Chemical ChemComp-TIN / 2-{(5-{[BUTYL-(2-CYCLOHEXYL-ETHYL)-AMINO]-METHYL}-2'-METHYL-BIPHENYL-2-CARBONYL)-AMINO]-4-METHYLSULFANYL-BUTYRIC ACID


Mass: 538.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H46N2O3S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.65 %
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→33.94 Å / Num. all: 15264 / Num. obs: 13304 / % possible obs: 87.4 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.72 Å / % possible all: 83.7

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.5→33.94 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1273 9.5 %Random
Rwork0.295 ---
all-15264 --
obs-13304 --
Refine analyzeLuzzati coordinate error obs: 0.47 Å / Luzzati sigma a obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 3.5→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 59 0 5873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.8
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_dihedral_angle_d19.1
X-RAY DIFFRACTIONx_improper_angle_d0.77
LS refinement shellResolution: 3.5→3.72 Å /
RfactorNum. reflection
Rfree0.317 200
Rwork0.321 -
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.77

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