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- PDB-2jle: Novel indazole nnrtis created using molecular template hybridizat... -

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Basic information

Entry
Database: PDB / ID: 2jle
TitleNovel indazole nnrtis created using molecular template hybridization based on crystallographic overlays
ComponentsREVERSE TRANSCRIPTASE/RNASEH
KeywordsTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / ENDONUCLEASE / METAL-BINDING / PHOSPHOPROTEIN / NUCLEASE / MYRISTATE / HYDROLASE / CYTOPLASM / MAGNESIUM / RNA-DIRECTED DNA POLYMERASE / CAPSID PROTEIN / DNA INTEGRATION / ASPARTYL PROTEASE / MULTIFUNCTIONAL ENZYME / RIBOSOMAL FRAMESHIFTING / CAPSID MATURATION / DNA RECOMBINATION / VIRAL NUCLEOPROTEIN / NUCLEOTIDYLTRANSFERASE / ZINC-FINGER / RNA-BINDING / LIPOPROTEIN / ZINC / AIDS / NNRTI / HIV-1 / VIRION / NUCLEUS / PROTEASE
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / aspartic-type endopeptidase activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / Ribonuclease H domain ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-I15 / Reverse transcriptase/RNaseH
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.9 Å
AuthorsJones, L.H. / Allan, G. / Barba, O. / Burt, C. / Corbau, R. / Dupont, T. / Irving, S. / Mowbray, C.E. / Phillips, C. / Swain, N.A. ...Jones, L.H. / Allan, G. / Barba, O. / Burt, C. / Corbau, R. / Dupont, T. / Irving, S. / Mowbray, C.E. / Phillips, C. / Swain, N.A. / Webster, R. / Westby, M.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Novel Indazole Non-Nucleoside Reverse Transcriptase Inhibitors Using Molecular Hybridization Based on Crystallographic Overlays.
Authors: Jones, L.H. / Allan, G. / Barba, O. / Burt, C. / Corbau, R. / Dupont, T. / Knochel, T. / Irving, S. / Middleton, D.S. / Mowbray, C.E. / Perros, M. / Ringrose, H. / Swain, N.A. / Webster, R. ...Authors: Jones, L.H. / Allan, G. / Barba, O. / Burt, C. / Corbau, R. / Dupont, T. / Knochel, T. / Irving, S. / Middleton, D.S. / Mowbray, C.E. / Perros, M. / Ringrose, H. / Swain, N.A. / Webster, R. / Westby, M. / Phillips, C.
History
DepositionSep 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE/RNASEH
B: REVERSE TRANSCRIPTASE/RNASEH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7403
Polymers130,4472
Non-polymers2921
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-31.25 kcal/mol
Surface area44520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.200, 154.600, 155.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein REVERSE TRANSCRIPTASE/RNASEH / REVERSE TRANSCRIPTASE


Mass: 65223.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: Z2/CDC-Z34 ISOLATE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q72547
#2: Chemical ChemComp-I15 / 5-[(5-fluoro-3-methyl-1H-indazol-4-yl)oxy]benzene-1,3-dicarbonitrile


Mass: 292.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H9FN4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 59.86 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→29 Å / Num. obs: 30525 / % possible obs: 96 % / Redundancy: 3 % / Biso Wilson estimate: 100.955 Å2 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: BUSTER-TNT / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.9→14.13 Å / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3512 1535 5.07 %RANDOM
Rwork0.2613 ---
obs0.2674 30263 96.72 %-
Displacement parametersBiso mean: 60.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.22782726 Å20 Å20 Å2
2--5.8471928 Å20 Å2
3----6.07502007 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7859 0 22 239 8120
LS refinement shellResolution: 2.9→3.07 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.4459 247 5.06 %
Rwork0.3252 4638 -
all0.3836 4885 -
obs--96.72 %

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