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- PDB-8est: REACTION OF PORCINE PANCREATIC ELASTASE WITH 7-SUBSTITUTED 3-ALKO... -

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Entry
Database: PDB / ID: 8est
TitleREACTION OF PORCINE PANCREATIC ELASTASE WITH 7-SUBSTITUTED 3-ALKOXY-4-CHLOROISOCOUMARINS: DESIGN OF POTENT INHIBITORS USING THE CRYSTAL STRUCTURE OF THE COMPLEX FORMED WITH 4-CHLORO-3-ETHOXY-7-GUANIDINO-ISOCOUMARIN
ComponentsPORCINE PANCREATIC ELASTASE
KeywordsHYDROLASE(SERINE PROTEINASE)
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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-GIS / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsRadhakrishnan, R. / Powers, J.C. / Meyerjunior, E.F.
Citation
Journal: Biochemistry / Year: 1990
Title: Reaction of porcine pancreatic elastase with 7-substituted 3-alkoxy-4-chloroisocoumarins: design of potent inhibitors using the crystal structure of the complex formed with 4-chloro-3-ethoxy-7- ...Title: Reaction of porcine pancreatic elastase with 7-substituted 3-alkoxy-4-chloroisocoumarins: design of potent inhibitors using the crystal structure of the complex formed with 4-chloro-3-ethoxy-7-guanidinoisocoumarin.
Authors: Powers, J.C. / Oleksyszyn, J. / Narasimhan, S.L. / Kam, C.M.
#1: Journal: J.Med.Chem. / Year: 1992
Title: Effect of the 7-Amino Substituent on the Inhibitory Potency of Mechanism-Based Isocoumarin Inhibitors for Porcine Pancreatic and Human Neutrophil Elastases: A 1.85-Angstroms X-Ray Structure of ...Title: Effect of the 7-Amino Substituent on the Inhibitory Potency of Mechanism-Based Isocoumarin Inhibitors for Porcine Pancreatic and Human Neutrophil Elastases: A 1.85-Angstroms X-Ray Structure of the Complex between Porcine Pancreatic Elastase and 7-[(N-Tosylphenylalanyl)Amino]-4-Chloro-3-Methoxyisocoumarin
Authors: Hernandez, M.A. / Powers, J.C. / Glinski, J. / Oleksyszyn, J. / Vijayalakshmi, J. / Meyerjunior, E.F.
#2: Journal: Biochemistry / Year: 1991
Title: Structural Study of Porcine Pancreatic Elastase Complexed with 7-Amino-3-(2-Bromoethoxy)-4-Chloroisocoumarin as a Nonreactivatable Doubly Covalent Enzyme-Inhibitor Complex
Authors: Vijayalakshmi, J. / Meyerjunior, E.F. / Kam, C.-M. / Powers, J.C.
#3: Journal: J.Am.Chem.Soc. / Year: 1990
Title: The 2.2-Angstrom Resolution X-Ray Crystal Structure of the Complex of Trypsin Inhibited by 4-Chloro-3-Ethoxy-7-Guanidinoisocoumarin: A Proposed Model of the Thrombin-Inhibitor Complex
Authors: Chow, M.M. / Meyerjunior, E.F. / Bode, W. / Kam, C.-M. / Radhakrishnan, R. / Vijayalakshmi, J. / Powers, J.C.
#4: Journal: Biochemistry / Year: 1989
Title: Human Leukocyte and Porcine Pancreatic Elastase: X-Ray Crystal Structures, Mechanism, Substrate Specificity, and Mechanism-Based Inhibitors
Authors: Bode, W. / Meyerjunior, E.F. / Powers, J.C.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal Structures of the Complex of Porcine Pancreatic Elastase with Two Valine-Derived Benzoxazinone Inhibitors
Authors: Radhakrishnan, R. / Presta, L.G. / Meyerjunior, E.F. / Wildonger, R.
#6: Journal: J.Am.Chem.Soc. / Year: 1985
Title: Stereospecific Reaction of 3-Methoxy-4-Chloro-7-Amino-Isocoumarin with Crystalline Porcine Pancreatic Elastase
Authors: Meyerjunior, E.F. / Presta, L.G. / Radhakrishnan, R.
History
DepositionFeb 21, 1990Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3644
Polymers25,9281
Non-polymers4363
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.620, 58.260, 75.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 ...1: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 (CZ,NH1,NH2), GLN 110 (CG,CD,OE1,NE2), ARG 125 (CG,CD,NE,CZ,NH1,NH2), SO4 247 (O1,O3).

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GIS / ETHYL-(2-CARBOXY-4-GUANIDINIUM-PHENYL)-CHLOROACETATE


Mass: 299.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14ClN3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS COMPLEX IS ONE OF THE BEST IRREVERSIBLE INHIBITORS THUS FAR REPORTED FOR PPE (KOBS/[I] = ...THIS COMPLEX IS ONE OF THE BEST IRREVERSIBLE INHIBITORS THUS FAR REPORTED FOR PPE (KOBS/[I] = 8100/(MOLE. SEC) ).
Has protein modificationY
Nonpolymer detailsTHE TITLE INHIBITOR HAS BEEN STUDIED IN TWO RELATED ENZYMES PPE AND BOVINE TRYPSIN (REFERENCE 3). ...THE TITLE INHIBITOR HAS BEEN STUDIED IN TWO RELATED ENZYMES PPE AND BOVINE TRYPSIN (REFERENCE 3). IN THE LATTER CASE, AS WOULD BE EXPECTED, THE POSITIVELY CHARGED GUANIDINIUM GROUP IS LOCATED IN TRYPSIN'S PRIMARY SPECIFICITY (S1) SITE BUT TWO BINDING MODES ARE EXHIBITED, SINGLY AND DOUBLY COVALENTLY LINKED TO TRYPSIN. CONVERSELY, THE COMPLEX PRESENTED IN THIS ENTRY IS FLIPPED APPROXIMATELY 180 DEGREE SO THAT THE GUANIDINIUM GROUP IS FOUND IN THE S2' SITE, H-BONDED TO THR E 41.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.78→7 Å / Rfactor Rwork: 0.17
Details: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ...Details: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 (CZ,NH1,NH2), GLN 110 (CG,CD,OE1,NE2), ARG 125 (CG,CD,NE,CZ,NH1,NH2), SO4 247 (O1,O3).
Refinement stepCycle: LAST / Resolution: 1.78→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 25 169 2016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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