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- PDB-3zt4: Small molecule inhibitors of the LEDGF site of HIV type 1 integra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zt4 | ||||||
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Title | Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design | ||||||
![]() | INTEGRASE | ||||||
![]() | TRANSFERASE / AIDS | ||||||
Function / homology | ![]() symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. / Newman, J. / Rhodes, D.I. / Vandergraaff, N. / Le, G. / Jones, E.D. / Smith, J.A. / Coates, J.A.V. / Thienthong, N. / Dolezal, O. ...Peat, T.S. / Newman, J. / Rhodes, D.I. / Vandergraaff, N. / Le, G. / Jones, E.D. / Smith, J.A. / Coates, J.A.V. / Thienthong, N. / Dolezal, O. / Ryan, J.H. / Savage, G.P. / Francis, C. / Deadman, J.J. | ||||||
![]() | ![]() Title: Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design Authors: Peat, T.S. / Rhodes, D.I. / Vandergraaff, N. / Le, G. / Smith, J.A. / Clark, L.J. / Jones, E.D. / Coates, J.A.V. / Thienthong, N. / Newman, J. / Dolezal, O. / Mulder, R. / Ryan, J.H. / ...Authors: Peat, T.S. / Rhodes, D.I. / Vandergraaff, N. / Le, G. / Smith, J.A. / Clark, L.J. / Jones, E.D. / Coates, J.A.V. / Thienthong, N. / Newman, J. / Dolezal, O. / Mulder, R. / Ryan, J.H. / Savage, G.P. / Francis, C.L. / Deadman, J.J. #1: ![]() Title: Structural Basis for a New Mechanism of Inhibition of HIV-1 Integrase Identified by Fragment Screening and Structure-Based Design. Authors: Rhodes, D.I. / Peat, T.S. / Vandegraaff, N. / Jeevarajah, D. / Le, G. / Jones, E.D. / Smith, J.A. / Coates, J.A. / Winfield, L.J. / Thienthong, N. / Newman, J. / Lucent, D. / Ryan, J.H. / ...Authors: Rhodes, D.I. / Peat, T.S. / Vandegraaff, N. / Jeevarajah, D. / Le, G. / Jones, E.D. / Smith, J.A. / Coates, J.A. / Winfield, L.J. / Thienthong, N. / Newman, J. / Lucent, D. / Ryan, J.H. / Savage, G.P. / Francis, C.L. / Deadman, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 61 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zcmC ![]() 3zsoC ![]() 3zsqC ![]() 3zsrC ![]() 3zsvC ![]() 3zswC ![]() 3zsxC ![]() 3zsyC ![]() 3zszC ![]() 3zt0C ![]() 3zt1C ![]() 3zt2C ![]() 3zt3C ![]() 3nf7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18395.842 Da / Num. of mol.: 2 / Fragment: CORE CATALYTIC DOMAIN, RESIDUES 56-212 / Mutation: YES Source method: isolated from a genetically manipulated source Details: INHIBITOR BOUND TO THE LEDGF SITE / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q76353, UniProt: P12497*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 5 types, 116 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZT2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZT2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-ZT2 / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 56 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 139 TO ASP ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 1, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→61.55 Å / Num. obs: 19132 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NF7 Resolution: 2.2→61.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.322 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.731 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→61.54 Å
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Refine LS restraints |
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