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- PDB-6ncj: Structure of HIV-1 Integrase with potent 5,6,7,8-Tetrahydro-1,6-n... -

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Basic information

Entry
Database: PDB / ID: 6ncj
TitleStructure of HIV-1 Integrase with potent 5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives Allosteric Site Inhibitors
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase / Catalytic / Inhibitor
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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. / Integrase core domain ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KJJ / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNolte, R.T.
CitationJournal: J. Med. Chem. / Year: 2019
Title: 5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives as Potent HIV-1-Integrase-Allosteric-Site Inhibitors.
Authors: Peese, K.M. / Allard, C.W. / Connolly, T. / Johnson, B.L. / Li, C. / Patel, M. / Sorensen, M.E. / Walker, M.A. / Meanwell, N.A. / McAuliffe, B. / Minassian, B. / Krystal, M. / Parker, D.D. / ...Authors: Peese, K.M. / Allard, C.W. / Connolly, T. / Johnson, B.L. / Li, C. / Patel, M. / Sorensen, M.E. / Walker, M.A. / Meanwell, N.A. / McAuliffe, B. / Minassian, B. / Krystal, M. / Parker, D.D. / Lewis, H.A. / Kish, K. / Zhang, P. / Nolte, R.T. / Simmermacher, J. / Jenkins, S. / Cianci, C. / Naidu, B.N.
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,6988
Polymers19,6851
Non-polymers1,0137
Water1,65792
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,39716
Polymers39,3712
Non-polymers2,02614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5420 Å2
ΔGint-40 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.290, 72.290, 64.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-453-

HOH

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Components

#1: Protein Integrase /


Mass: 19685.273 Da / Num. of mol.: 1 / Mutation: C56S, F139D, F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2WR52
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-KJJ / (2~{S})-2-[4-(8-fluoranyl-5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)-2-methyl-6-[[(1~{S},2~{R})-2-phenylcyclopropyl]methyl]-7,8-dihydro-5~{H}-1,6-naphthyridin-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid


Mass: 572.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H41FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The optimized conditions consisted of a reservoir solution with 1.8 - 2.2 M ammonium sulfate and 100 mM sodium acetate pH 4.6 - 5.5. Drops were formed from 0.3 mL of the protein solution and ...Details: The optimized conditions consisted of a reservoir solution with 1.8 - 2.2 M ammonium sulfate and 100 mM sodium acetate pH 4.6 - 5.5. Drops were formed from 0.3 mL of the protein solution and 0.3 mL of the reservoir solution (total initial volume of 0.6 mL), mixed, and placed at 20C to equilibrate.
PH range: 4.6 - 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.99 Å / Num. obs: 13589 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 28.46 Å2 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.011 / Rrim(I) all: 0.033 / Χ2: 0.966 / Net I/σ(I): 36.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 668 / CC1/2: 0.785 / Rpim(I) all: 0.329 / Rrim(I) all: 0.974 / Χ2: 0.871 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 2→31.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.157 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.24 643 4.76 %RANDOM
Rwork0.194 ---
obs0.196 13507 99.7 %-
Displacement parametersBiso max: 121.4 Å2 / Biso mean: 32.25 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.1402 Å20 Å20 Å2
2--1.1402 Å20 Å2
3----2.2803 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 68 92 1243
Biso mean--34.4 47.92 -
Num. residues----142
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d387SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes194HARMONIC5
X-RAY DIFFRACTIONt_it1190HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1459SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1190HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1615HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion16.24
LS refinement shellResolution: 2→2.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.2699 13 3.07 %
Rwork0.2848 410 -
all0.2843 423 -
obs--93.76 %

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