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- PDB-8vrp: HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold... -

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Basic information

Entry
Database: PDB / ID: 8vrp
TitleHIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor
ComponentsSpacer peptide 1
KeywordsVIRAL PROTEIN / HIV-1 / Human Immunodeficiency Virus / Capsid / HIV-CA / Capsid Inhibitor / HIV Restriction
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
: / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoldstone, D.C. / Walsham, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of 4-Quinazolinone-bearing Phenylalanine Derivatives as HIV-1 Capsid Inhibitors with Potent and Insensitivity Towards Clinically Relevant Resistant Mutations
Authors: Zhang, X. / Walsham, L. / Zhan, P. / Goldstone, D.C.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spacer peptide 1
C: Spacer peptide 1
A: Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,19210
Polymers75,7473
Non-polymers3,4457
Water5,945330
1
B: Spacer peptide 1
C: Spacer peptide 1
hetero molecules

B: Spacer peptide 1
C: Spacer peptide 1
hetero molecules

B: Spacer peptide 1
C: Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,51221
Polymers151,4946
Non-polymers7,01815
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area25610 Å2
ΔGint-96 kcal/mol
Surface area60770 Å2
MethodPISA
2
A: Spacer peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,13118
Polymers151,4946
Non-polymers6,63712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_345-y-2,x-y-1,z1
crystal symmetry operation3_435-x+y-1,-x-2,z1
crystal symmetry operation4_335-x-2,-y-2,z1
crystal symmetry operation5_545y,-x+y-1,z1
crystal symmetry operation6_455x-y-1,x,z1
Buried area24100 Å2
ΔGint-92 kcal/mol
Surface area60500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.268, 160.268, 57.235
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Spacer peptide 1 / SP1 / p2


Mass: 25248.982 Da / Num. of mol.: 3 / Mutation: A14C, E45C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR(DE3) / References: UniProt: P12493
#2: Chemical ChemComp-A1ADQ / N-[(1S)-1-[(3P,7M)-3-{4-chloro-3-[(ethanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-7-(3-fluoro-4-formylphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-yl]acetamide


Mass: 979.268 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H32ClF9N8O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Morpheus condition B2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.8→46.618 Å / Num. obs: 78027 / % possible obs: 100 % / Redundancy: 42.3 % / CC1/2: 0.998 / Rpim(I) all: 0.049 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 43.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4429 / CC1/2: 0.441 / Rpim(I) all: 2.231 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.618 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.089 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2257 3905 5.005 %
Rwork0.1924 74120 -
all0.194 --
obs-78025 99.991 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.022 Å2-0.011 Å2-0 Å2
2---0.022 Å20 Å2
3---0.071 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 205 330 5631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165081
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.8337456
X-RAY DIFFRACTIONr_angle_other_deg0.6051.7511730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74410.450
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg27.148159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80810892
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.71310221
X-RAY DIFFRACTIONr_chiral_restr0.090.2813
X-RAY DIFFRACTIONr_chiral_restr_other0.0010.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021160
X-RAY DIFFRACTIONr_nbd_refined0.2340.21207
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24556
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22735
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.236
X-RAY DIFFRACTIONr_nbd_other0.2120.2156
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.223
X-RAY DIFFRACTIONr_mcbond_it3.2433.3292653
X-RAY DIFFRACTIONr_mcbond_other3.243.3282652
X-RAY DIFFRACTIONr_mcangle_it4.565.9753312
X-RAY DIFFRACTIONr_mcangle_other4.565.9773313
X-RAY DIFFRACTIONr_scbond_it4.5913.7292798
X-RAY DIFFRACTIONr_scbond_other4.593.732799
X-RAY DIFFRACTIONr_scangle_it6.9956.6134142
X-RAY DIFFRACTIONr_scangle_other6.9946.6124143
X-RAY DIFFRACTIONr_lrange_it8.3235.9326444
X-RAY DIFFRACTIONr_lrange_other8.28935.6366396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.8-1.8470.3273020.31154670.31257690.9220.930.3
1.847-1.8970.3232380.28652870.28855250.9290.9430.272
1.897-1.9520.2892910.27151690.27254600.9380.9510.252
1.952-2.0120.2792660.24349900.24552560.9470.9610.219
2.012-2.0780.2712330.22348880.22651210.9530.9690.198
2.078-2.1510.2592400.20347050.20649450.9590.9740.18
2.151-2.2320.2212620.19545370.19747990.9690.9770.172
2.232-2.3230.2462880.18943080.19345960.9630.9780.167
2.323-2.4260.2232330.18141850.18344180.9710.9810.161
2.426-2.5440.2392050.18940170.19242220.9690.980.17
2.544-2.6810.2461960.19638170.19840130.9690.9790.178
2.681-2.8430.2152060.17736090.17938150.9740.9820.164
2.843-3.0380.2211610.18334410.18536020.9690.980.177
3.038-3.2810.241520.19431950.19633470.9670.9770.193
3.281-3.5920.2041540.18729390.18830930.9770.9810.192
3.592-4.0130.2161180.1826760.18227940.9730.9830.193
4.013-4.6280.1981270.15623620.15824890.9820.9870.179
4.628-5.6540.18860.17720370.17721230.9810.9850.205
5.654-7.9380.205930.18115640.18216570.9810.9840.209
7.938-46.6180.175540.1729270.1729810.9850.9820.208

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