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- PDB-1n95: Aryl Tetrahydrophyridine Inhbitors of Farnesyltranferase: Glycine... -

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Basic information

Entry
Database: PDB / ID: 1n95
TitleAryl Tetrahydrophyridine Inhbitors of Farnesyltranferase: Glycine, Phenylalanine and Histidine Derivatives
Components
  • Protein farnesyltransferase alpha subunit
  • Protein farnesyltransferase beta subunit
KeywordsTRANSFERASE / Farnesyltransferase / histidine tetrahydropyridine / 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 / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of fibroblast proliferation / regulation of microtubule-based movement / geranylgeranyl diphosphate synthase activity / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / wound healing / receptor tyrosine kinase binding / lipid metabolic process / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / molecular adaptor activity / cell population proliferation / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / 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 alpha-alpha toroid domain / 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 alpha-alpha toroid domain / 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
Chem-FTH / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID / 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: 2.3 Å
AuthorsGwaltney II, S.L. / O'Conner, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)83,8685
Polymers82,9932
Non-polymers8743
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-59 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.126, 171.126, 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 farnesyltransferase alpha subunit / RAS proteins prenyltransferase alpha / FTase-alpha


Mass: 38016.711 Da / Num. of mol.: 1 / Fragment: residue 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 farnesyltransferase beta subunit / RAS proteins prenyltransferase beta / FTase-beta


Mass: 44976.410 Da / Num. of mol.: 1 / Fragment: residue 22-423
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HFP / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID


Mass: 308.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H33O4P
#5: Chemical ChemComp-FTH / 1-[2-(4-CYANO-BENZYLAMINO)-3-(3-METHYL-3H-IMIDAZOL-4-YL)-PROPIONYL]-5-NAPHTHALEN-1-YL-1,2,3,6-TETRAHYDRO-PYRIDINE-4-CARBONITRILE


Mass: 500.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H28N6O

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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: 3.57 Å3/Da / Density % sol: 65.26 %
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: Apr 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→43.59 Å / Num. all: 51808 / Num. obs: 43175 / % possible obs: 83.4 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.4 Å / % possible all: 64

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→43.59 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.358 4340 random
Rwork0.337 --
all-51808 -
obs-43175 -
Refine analyzeLuzzati coordinate error obs: 0.52 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 59 0 5873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONx_angle_d1.8
X-RAY DIFFRACTIONt_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_improper_angle_d1
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.1
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg1

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