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- PDB-1ohr: VIRACEPT (R) (NELFINAVIR MESYLATE, AG1343): A POTENT ORALLY BIOAV... -

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Basic information

Entry
Database: PDB / ID: 1ohr
TitleVIRACEPT (R) (NELFINAVIR MESYLATE, AG1343): A POTENT ORALLY BIOAVAILABLE INHIBITOR OF HIV-1 PROTEASE
ComponentsASPARTYLPROTEASE
KeywordsASPARTYL PROTEASE / HYDROLASE / HIV-I PROTEASE
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-1UN / V-1 PROTEASE protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsDavies II, J.F.
CitationJournal: J.Med.Chem. / Year: 1997
Title: Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease.
Authors: Kaldor, S.W. / Kalish, V.J. / Davies 2nd., J.F. / Shetty, B.V. / Fritz, J.E. / Appelt, K. / Burgess, J.A. / Campanale, K.M. / Chirgadze, N.Y. / Clawson, D.K. / Dressman, B.A. / Hatch, S.D. / ...Authors: Kaldor, S.W. / Kalish, V.J. / Davies 2nd., J.F. / Shetty, B.V. / Fritz, J.E. / Appelt, K. / Burgess, J.A. / Campanale, K.M. / Chirgadze, N.Y. / Clawson, D.K. / Dressman, B.A. / Hatch, S.D. / Khalil, D.A. / Kosa, M.B. / Lubbehusen, P.P. / Muesing, M.A. / Patick, A.K. / Reich, S.H. / Su, K.S. / Tatlock, J.H.
History
DepositionSep 27, 1997Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: ASPARTYLPROTEASE
B: ASPARTYLPROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1753
Polymers21,6082
Non-polymers5681
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-32 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.040, 59.380, 61.670
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 ASPARTYLPROTEASE


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH VIRACEPT / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Q288
#2: Chemical ChemComp-1UN / 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE / NELFINAVIR MESYLATE AG1343


Mass: 567.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H45N3O4S / Comment: medication, antiretroviral, protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / Rfactor Rwork: 0.2 / Rfactor obs: 0.2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 44 153 1952
Refine LS restraints NCSNCS model details: RESTRAINTS

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