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- PDB-20xx: HIV-1 integrase core domain in complex with potent allosteric inh... -

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Basic information

Entry
Database: PDB / ID: 20xx
TitleHIV-1 integrase core domain in complex with potent allosteric inhibitors
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Inhibitor / Compplex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNomura, A. / Orita, T. / Furuzono, T. / Adachi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery and optimization of novel and potent allosteric HIV-1 integrase inhibitors with a spiro[indene] moiety
Authors: Adachi, K. / Manabe, T. / Yamasaki, T. / Suma, A. / Oghoshi, Y. / Takahashi, A. / Orita, T. / Nomura, A. / Adachi, T. / Ohata, Y. / Akiyama, Y. / Miyazaki, S.
History
DepositionDec 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3676
Polymers18,4441
Non-polymers9235
Water79344
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,73312
Polymers36,8872
Non-polymers1,84610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)72.030, 72.030, 66.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Integrase / IN


Mass: 18443.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HIV intagrase core domain
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-A1MCX / (2~{S})-2-[(3~{a}~{R},7~{a}~{R})-1'-ethyl-5'-methyl-spiro[1,3,3~{a},4,5,6,7,7~{a}-octahydroindene-2,3'-indene]-4'-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid


Mass: 396.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium cacodylate, 0.2 M ammonium sulfate, 20% (w/v) PEG8000, 25% (w/v) PEG 200 and 5 mM DTT solution and flash-frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→62.38 Å / Num. obs: 10448 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 24.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 770 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.01 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.3413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 501 4.8 %
Rwork0.231 9926 -
obs0.232 10427 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 57 44 1178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121168
X-RAY DIFFRACTIONf_angle_d1.60681591
X-RAY DIFFRACTIONf_chiral_restr0.0961181
X-RAY DIFFRACTIONf_plane_restr0.0081188
X-RAY DIFFRACTIONf_dihedral_angle_d19.3552422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.28811220.26082434X-RAY DIFFRACTION100
2.42-2.770.27681440.26772448X-RAY DIFFRACTION99.96
2.77-3.490.26061150.24062478X-RAY DIFFRACTION100
3.49-36.010.22831200.20972566X-RAY DIFFRACTION99.33

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