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- PDB-9b2h: HIV-1 wild type protease with GRL-072-17A, a substituted tetrahyd... -

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Basic information

Entry
Database: PDB / ID: 9b2h
TitleHIV-1 wild type protease with GRL-072-17A, a substituted tetrahydrofuran derivative based on Darunavir as P2 group
ComponentsProtease
KeywordsVIRAL PROTEIN / ASPARTIC ACID PROTEASE / HIV-1 protease / Darunavir / a substituted Tetrahydrofuran derivative inhibitor
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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
: / FORMIC ACID / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsWang, Y.-F. / Agniswamy, J. / Ghosh, A.K. / Weber, I.T.
Funding support United States, Japan, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150466 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150461 United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
Japan Agency for Medical Research and Development (AMED)JP15fk0410001, JP16fk0410101 Japan
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
National Center for Global Health and Medicine (NCGM) Research Institute Japan
Welfare and Labor of Japan Japan
Grant-in-Aid for Scientific Research and a Grant-in-Aid for Challenging Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (Monbu Kagakusho) Japan
CitationJournal: Org.Biomol.Chem. / Year: 2024
Title: Design of substituted tetrahydrofuran derivatives for HIV-1 protease inhibitors: synthesis, biological evaluation, and X-ray structural studies.
Authors: Ghosh, A.K. / Lee, D. / Sharma, A. / Johnson, M.E. / Ghosh, A.K. / Wang, Y.F. / Agniswamy, J. / Amano, M. / Hattori, S.I. / Weber, I.T. / Mitsuya, H.
History
DepositionMar 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,50412
Polymers21,4812
Non-polymers1,02310
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-81 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.576, 85.877, 46.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease


Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pJ414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RZ08, HIV-1 retropepsin

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Non-polymers , 6 types, 221 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-A1AIH / 2,5:6,9-dianhydro-1,3,7,8-tetradeoxy-4-O-({(2S,3R)-3-hydroxy-4-[(4-methoxybenzene-1-sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamoyl)-L-gluco-nonitol


Mass: 604.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H44N2O8S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.7M NaCl, 0.1M Sodium Acetate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 51438 / % possible obs: 93.6 % / Redundancy: 5.8 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.04 / Rrim(I) all: 0.098 / Χ2: 1 / Net I/σ(I): 19.5 / Num. measured all: 296116
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.32-1.374.80.51238560.8740.9660.2480.5711.00671.5
1.37-1.425.80.3650040.9520.9880.160.395192.5
1.42-1.496.10.27452270.9720.9930.1190.2990.99796
1.49-1.575.90.18552120.9820.9960.0810.2020.99296.2
1.57-1.665.50.13552200.9850.9960.0620.1490.99495.7
1.66-1.795.90.10352450.9870.9970.0450.1121.00595.9
1.79-1.9760.0853320.9920.9980.0350.0871.00697.5
1.97-2.265.70.07353840.9920.9980.0330.0811.00497.4
2.26-2.845.90.0753170.9930.9980.0310.0770.99895.8
2.84-505.70.08656410.9820.9950.0390.0941.00297

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASER2.8.2phasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→36.36 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.228 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16358 2566 5 %RANDOM
Rwork0.13011 ---
obs0.13174 48778 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20 Å2
2---0.44 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.32→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 63 211 1786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131797
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171847
X-RAY DIFFRACTIONr_angle_refined_deg2.1731.7122477
X-RAY DIFFRACTIONr_angle_other_deg1.4311.6434318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9722.72766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1115331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.476159
X-RAY DIFFRACTIONr_chiral_restr0.1320.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02337
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0281.331857
X-RAY DIFFRACTIONr_mcbond_other2.0291.332858
X-RAY DIFFRACTIONr_mcangle_it2.442.0091082
X-RAY DIFFRACTIONr_mcangle_other2.4452.011083
X-RAY DIFFRACTIONr_scbond_it3.5641.747940
X-RAY DIFFRACTIONr_scbond_other3.5531.746939
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7642.4541374
X-RAY DIFFRACTIONr_long_range_B_refined3.58316.5231794
X-RAY DIFFRACTIONr_long_range_B_other3.48916.11758
X-RAY DIFFRACTIONr_rigid_bond_restr4.4933644
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.324→1.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 137 -
Rwork0.183 2413 -
obs--62.84 %

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