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- PDB-1eat: NONPEPTIDIC INHIBITORS OF HUMAN LEUKOCYTE ELASTASE. 5. DESIGN, SY... -

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Entry
Database: PDB / ID: 1eat
TitleNONPEPTIDIC INHIBITORS OF HUMAN LEUKOCYTE ELASTASE. 5. DESIGN, SYNTHESIS, AND X-RAY CRYSTALLOGRAPHY OF A SERIES OF ORALLY ACTIVE 5-AMINO-PYRIMIDIN-6-ONE-CONTAINING TRIFLUOROMETHYLKETONES
ComponentsPORCINE PANCREATIC ELASTASE
KeywordsHYDROLASE (SERINE PROTEASE)
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-TFI / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCeccarelli, C.
Citation
Journal: J.Med.Chem. / Year: 1995
Title: Nonpeptidic inhibitors of human leukocyte elastase. 5. Design, synthesis, and X-ray crystallography of a series of orally active 5-aminopyrimidin-6-one-containing trifluoromethyl ketones.
Authors: Veale, C.A. / Bernstein, P.R. / Bryant, C. / Ceccarelli, C. / Damewood Jr., J.R. / Earley, R. / Feeney, S.W. / Gomes, B. / Kosmider, B.J. / Steelman, G.B. / Thomas, R.M. / Vacek, E.P. / ...Authors: Veale, C.A. / Bernstein, P.R. / Bryant, C. / Ceccarelli, C. / Damewood Jr., J.R. / Earley, R. / Feeney, S.W. / Gomes, B. / Kosmider, B.J. / Steelman, G.B. / Thomas, R.M. / Vacek, E.P. / Williams, J.C. / Wolanin, D.J. / Woolson, S.
#1: Journal: To be Published
Title: Nonpeptidic Inhibitors of Human Leukocyte Elastase. 6. Design of a Potent, Intratracheally Active, Pyridone-Based Trifluoromethyl Ketone
Authors: Bernstein, P.R. / Gomes, B.C. / Kosmider, B.J. / Vacek, E.P. / Williams, J.C.
#2: Journal: To be Published
Title: Nonpeptidic Inhibitors of Human Leukocyte Elastase. 4. Design, Synthesis,in Vitro, and in Vivo Activity of a Series of Beta-Carbolinone-Containing Trifluoromethyl Ketones
Authors: Veale, C.A. / Damewood, J.R. / Steelman, G.B. / Bryant, C. / Gomes, B. / Williams, J.
#3: Journal: J.Med.Chem. / Year: 1994
Title: Nonpeptidic Inhibitors of Human Leukocyte Elastase. 3. Design, Synthesis, X-Ray Crystallographic Analysis, and Structure-Activity Relationships for a Series of Orally Active 3-Amino-6- ...Title: Nonpeptidic Inhibitors of Human Leukocyte Elastase. 3. Design, Synthesis, X-Ray Crystallographic Analysis, and Structure-Activity Relationships for a Series of Orally Active 3-Amino-6-Phenylpyridin-2-One Trifluoromethyl Ketones
Authors: Bernstein, P.R. / Andisik, D. / Bradley, P.K. / Bryant, C.B. / Ceccarelli, C. / Damewood, J.R. / Earley, R. / Edwards, P.D. / Feeney, S. / Gomes, B.C. / Kosmider, B.J. / Steelman, G.B. / ...Authors: Bernstein, P.R. / Andisik, D. / Bradley, P.K. / Bryant, C.B. / Ceccarelli, C. / Damewood, J.R. / Earley, R. / Edwards, P.D. / Feeney, S. / Gomes, B.C. / Kosmider, B.J. / Steelman, G.B. / Thomas, R.M. / Vacek, E.P. / Veale, C.A. / Williams, J.C. / Wolanin, D.J. / Woolson, S.A.
#4: Journal: J.Med.Chem. / Year: 1994
Title: Nonpeptidic Inhibitors of Human Leukocyte Elastase. 2. Design, Synthesis and in Vitro Activity of a Series of 3-Amino-6-Arylpyridin-2-One Trifluoromethyl Ketones
Authors: Damewood, J.R. / Edwards, P.D. / Feeney, S. / Gomes, B.C. / Steelman, G.B. / Tuthill, P.A. / Warner, P. / Williams, J.C. / Woolson, S.A. / Wolanin, D. / Veale, C.
#5: Journal: J.Med.Chem. / Year: 1994
Title: Nonpeptidic Inhibitors of Human Leukocyte Elastase. 1. The Design and Synthesis of Pyridone-Containing Inhibitors
Authors: Warner, P. / Green, R.C. / Gomes, B.C. / Williams, J.C.
#6: Journal: J.Med.Chem. / Year: 1994
Title: Design of Orally Active, Nonpeptidic Inhibitors of Human Leukocyte Elastase
Authors: Brown, F.J. / Andisik, D.W. / Bernstein, P.R. / Bryant, C.B. / Ceccarelli, C. / Damewood, J.R. / Edwards, P.D. / Earley, R. / Feeney, S.W. / Green, R.C. / Gomes, B. / Kosmider, B.J. / Krell, ...Authors: Brown, F.J. / Andisik, D.W. / Bernstein, P.R. / Bryant, C.B. / Ceccarelli, C. / Damewood, J.R. / Edwards, P.D. / Earley, R. / Feeney, S.W. / Green, R.C. / Gomes, B. / Kosmider, B.J. / Krell, R. / Shaw, A. / Steelman, G.B. / Thomas, R.M. / Vacek, E.P. / Veale, C.A. / Tuthill, P.A. / Warner, P. / Williams, J.C. / Wolanin, D.J. / Woolson, S.A.
#7: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Design, Synthesis, and Kinetic Evaluation of a Unique Class of Elastase Inhibitors, the Peptidyl Alpha-Ketobenzoxazoles,and the X-Ray Crystal Structure of the Covalent Complex between Porcine ...Title: Design, Synthesis, and Kinetic Evaluation of a Unique Class of Elastase Inhibitors, the Peptidyl Alpha-Ketobenzoxazoles,and the X-Ray Crystal Structure of the Covalent Complex between Porcine Pancreatic Elastase and Ac-Ala-Pro-Val-2-Benzoxazole
Authors: Edwards, P.D. / Meyer, E.F. / Vijayalakshmi, J. / Tuthill, P.A. / Andisik, D.A. / Gomes, B. / Strimpler, A.
#8: Journal: J.Am.Chem.Soc. / Year: 1989
Title: Crystal Structure of the Covalent Complex Formed by a Peptidyl Alpha,Alpha-Difluoro-Beta-Keto Amide with Porcine Pancreatic Elastase at 1.78-Angstrom Resolution
Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfield, R.E. / Meyer, E.F. / Trainor, D.A.
#9: Journal: J.Mol.Biol. / Year: 1988
Title: X-Ray Diffraction Analysis of the Inhibition of Porcine Pancreatic Elastase by a Peptidyl Trifluoromethylketone
Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfield, R.E. / Meyer, E.F. / Trainor, D.A. / Stein, M.
History
DepositionNov 22, 1994-
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6335
Polymers25,9281
Non-polymers7054
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.990, 57.790, 75.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PORCINE PANCREATIC ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TFI / 2-[5-METHANESULFONYLAMINO-2-(4-AMINOPHENYL)-6-OXO-1,6-DIHYDRO-1-PYRIMIDINYL]-N-(3,3,3-TRIFLUORO-1-ISOPROPYL-2-OXOPROPYL)ACETAMIDE


Mass: 489.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22F3N5O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsC2 OF HET GROUP TFK IS COVALENTLY BONDED TO O-GAMMA OF SER 195.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 13563 / % possible obs: 85 % / Observed criterion σ(F): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.167 --
obs0.167 11807 85 %
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 44 126 1992
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_d1.561.58
X-RAY DIFFRACTIONx_improper_angle_d1.8

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