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- PDB-2xye: HIV-1 Inhibitors with a Tertiary-Alcohol-containing Transition-St... -

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Basic information

Entry
Database: PDB / ID: 2xye
TitleHIV-1 Inhibitors with a Tertiary-Alcohol-containing Transition-State Mimic and various P2 and P1 prime Substituents
ComponentsPROTEASE
KeywordsHYDROLASE / AIDS
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-CXG / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOhrngren, P. / Wu, X. / Persson, M. / Ekegren, J.K. / Wallberg, H. / Rosenquist, A. / Samuelsson, B. / Unge, T. / Larhed, M.
CitationJournal: Med.Chem.Commun. / Year: 2011
Title: HIV-1 Protease Inhibitors with a Tertiary Alcohol Containing Transition-State Mimic and Various P2 and P1' Substituents
Authors: Ohrngren, P. / Wu, X. / Persson, M. / Ekegren, J.K. / Wallberg, H. / Vrang, L. / Rosenquist, A. / Samuelsson, B. / Unge, T. / Larhed, M.
History
DepositionNov 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Other
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2533
Polymers21,5512
Non-polymers7021
Water2,378132
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-23.4 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.130, 85.860, 46.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEASE / PR / RETROPEPSIN


Mass: 10775.659 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 (Z2/CDC-Z34 ISOLATE)
Strain: D10 / Description: GROUP M SUBTYPE D / Plasmid: PEXP5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-AI
References: UniProt: P03366, UniProt: P12499*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-CXG / METHYL N-[(2S)-1-[2-[(4R)-5-[[(2S)-3,3-DIMETHYL-1-METHYLAMINO-1-OXO-BUTAN-2-YL]AMINO]-4-HYDROXY-5-OXO-4-(PHENYLMETHYL)PENTYL]-2-[(4-PHENYLPHENYL)METHYL]HYDRAZINYL]-3,3-DIMETHYL-1-OXO-BUTAN-2-YL]CARBAMATE


Mass: 701.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H55N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 563 TO PRO ENGINEERED RESIDUE IN CHAIN A, VAL 582 TO THR ...ENGINEERED RESIDUE IN CHAIN A, LEU 563 TO PRO ENGINEERED RESIDUE IN CHAIN A, VAL 582 TO THR ENGINEERED RESIDUE IN CHAIN A, ILE 584 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 563 TO PRO ENGINEERED RESIDUE IN CHAIN B, VAL 582 TO THR ENGINEERED RESIDUE IN CHAIN B, ILE 584 TO VAL

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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: 2.7 Å3/Da / Density % sol: 53.8 % / Description: NONE
Crystal growpH: 5
Details: PROTEASE 2MG/ML. PRECIPITANT 0.7M NACL, 100MM MES PH5.5

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0214
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0214 Å / Relative weight: 1
ReflectionResolution: 2→57.7 Å / Num. obs: 16091 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.5
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.7 / % possible all: 86.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WL0

2wl0


Resolution: 2→24.07 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1340973.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 799 5 %RANDOM
Rwork0.221 ---
obs0.221 15969 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7284 Å2 / ksol: 0.391824 e/Å3
Displacement parametersBiso mean: 13.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---2.05 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 51 132 1695
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 125 4.8 %
Rwork0.212 2462 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMINH.TOP
X-RAY DIFFRACTION3INH.PARWATER.TOP

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