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- PDB-8fui: HIV-1 wild type protease with GRL-02519A, with N-(2,5-dimethylphe... -

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Basic information

Entry
Database: PDB / ID: 8fui
TitleHIV-1 wild type protease with GRL-02519A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group
ComponentsProtease
KeywordsHYDROLASE/INHIBITOR / ASPARTIC ACID PROTEASE / HIV-1 PROTEASE / INHIBITORS / pyridylpyrimidine / HYDROLASE-INHIBITOR complex
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
ACETATE ION / FORMIC ACID / Chem-Y9R / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsWang, Y.-F. / Wong-Sam, A.E. / Ghosh, A.K. / Weber, I.T.
Funding support United States, 2items
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
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation.
Authors: Ghosh, A.K. / Mishevich, J.L. / Kovela, S. / Shaktah, R. / Ghosh, A.K. / Johnson, M. / Wang, Y.F. / Wong-Sam, A. / Agniswamy, J. / Amano, M. / Takamatsu, Y. / Hattori, S.I. / Weber, I.T. / Mitsuya, H.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,59213
Polymers21,4812
Non-polymers1,11111
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-81 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.451, 86.136, 46.113
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 / Strain: isolate BRU/LAI / Gene: pol / Plasmid: pJ414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RZ08, HIV-1 retropepsin

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Non-polymers , 7 types, 261 molecules

#2: Chemical ChemComp-Y9R / N-{(2S,3R)-4-[(4-aminobenzene-1-sulfonyl)(2-methylpropyl)amino]-3-hydroxy-1-phenylbutan-2-yl}-4-methyl-3-{[(4P)-4-(pyridin-3-yl)pyrimidin-2-yl]amino}benzamide


Mass: 679.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H41N7O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 1.1 M NaCl, 0.1 M Sodium Acetate, pH 5.4

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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: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 60036 / % possible obs: 92.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 13.999 Å2 / Rmerge(I) obs: 0.104 / Χ2: 0.045 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.25-1.291.70.38332091.001150.1
1.29-1.352.90.36351071.009179.6
1.35-1.414.70.34861410.996195.2
1.41-1.485.90.30263681.007198.7
1.48-1.576.10.22564250.995199.6
1.57-1.76.10.16764361.01199.2
1.7-1.876.60.13664830.995199.8
1.87-2.146.20.11165241.001199.8
2.14-2.696.30.09965401.001199
2.69-506.20.09268031.01198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.3 Å33.38 Å
Translation5.3 Å33.38 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER4.064phasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NU3

3nu3


Resolution: 1.25→33.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.514 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17555 3079 5.1 %RANDOM
Rwork0.13898 ---
obs0.14083 56906 92.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---1.08 Å20 Å2
3---1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.25→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 71 250 1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121882
X-RAY DIFFRACTIONr_bond_other_d0.0070.0161884
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.7132602
X-RAY DIFFRACTIONr_angle_other_deg0.6711.6144414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.36358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5510341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022117
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02363
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_it2.4361.474891
X-RAY DIFFRACTIONr_mcbond_other2.4351.477892
X-RAY DIFFRACTIONr_mcangle_it3.1082.221132
X-RAY DIFFRACTIONr_mcangle_other3.1082.2221133
X-RAY DIFFRACTIONr_scbond_it5.9671.928991
X-RAY DIFFRACTIONr_scbond_other5.9731.924988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9982.711448
X-RAY DIFFRACTIONr_long_range_B_refined6.50523.9351974
X-RAY DIFFRACTIONr_long_range_B_other6.50621.1891912
X-RAY DIFFRACTIONr_rigid_bond_restr18.09633766
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 131 -
Rwork0.341 2069 -
obs--46.24 %

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