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seesar v12.1  (BioSolveIT GmbH)

 
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    Structured Review

    BioSolveIT GmbH seesar v12.1
    Inclusion of RAL into CDs. A) The structure <t>of</t> <t>βCD</t> is used from the crystallography (PDB ID 3GCT). Those of RAM-βCD and HP-βCD are produced by the addition of side chains, 6-methyl and 6-hydroxypropyl groups, respectively, to the βCD, and representative binding models of RAL to βCD, RAM-βCD, and HP-βCD are generated by <t>SeeSAR.</t> Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. B) SPR illustrated the interaction of the drugs with multi-NH 2 -βCDs immobilized on a sensor chip. Sensorgrams of each concentration of RAL on the middle and BIC on the right side interacting with multi-NH 2 -βCDs are detected. C) The representative m / z spectra of RAL shown by the green arrow, BIC by the purple arrow, RAL plus βCD, RAL plus RAM-βCD, and RAL plus HP-βCD by the red arrows, are detected by ESI-MS. The spectra of RAL plus βCD are mostly found by adding Na+ or NH 4 + to RAL plus βCD. The different m / z spectra of RAL plus RAM-βCD and RAL plus HP-βCD are shown because each RAM-βCD and HP-βCD contains a different number of side chains.
    Seesar V12.1, supplied by BioSolveIT GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/seesar+v12%2E1/pmc10758923-160-36-38?v=BioSolveIT+GmbH
    Average 90 stars, based on 1 article reviews
    seesar v12.1 - by Bioz Stars, 2026-07
    90/100 stars

    Images

    1) Product Images from "Conversion of raltegravir carrying a 1,3,4-oxadiazole ring to a hydrolysis product upon pH changes decreases its antiviral activity"

    Article Title: Conversion of raltegravir carrying a 1,3,4-oxadiazole ring to a hydrolysis product upon pH changes decreases its antiviral activity

    Journal: PNAS Nexus

    doi: 10.1093/pnasnexus/pgad446

    Inclusion of RAL into CDs. A) The structure of βCD is used from the crystallography (PDB ID 3GCT). Those of RAM-βCD and HP-βCD are produced by the addition of side chains, 6-methyl and 6-hydroxypropyl groups, respectively, to the βCD, and representative binding models of RAL to βCD, RAM-βCD, and HP-βCD are generated by SeeSAR. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. B) SPR illustrated the interaction of the drugs with multi-NH 2 -βCDs immobilized on a sensor chip. Sensorgrams of each concentration of RAL on the middle and BIC on the right side interacting with multi-NH 2 -βCDs are detected. C) The representative m / z spectra of RAL shown by the green arrow, BIC by the purple arrow, RAL plus βCD, RAL plus RAM-βCD, and RAL plus HP-βCD by the red arrows, are detected by ESI-MS. The spectra of RAL plus βCD are mostly found by adding Na+ or NH 4 + to RAL plus βCD. The different m / z spectra of RAL plus RAM-βCD and RAL plus HP-βCD are shown because each RAM-βCD and HP-βCD contains a different number of side chains.
    Figure Legend Snippet: Inclusion of RAL into CDs. A) The structure of βCD is used from the crystallography (PDB ID 3GCT). Those of RAM-βCD and HP-βCD are produced by the addition of side chains, 6-methyl and 6-hydroxypropyl groups, respectively, to the βCD, and representative binding models of RAL to βCD, RAM-βCD, and HP-βCD are generated by SeeSAR. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. B) SPR illustrated the interaction of the drugs with multi-NH 2 -βCDs immobilized on a sensor chip. Sensorgrams of each concentration of RAL on the middle and BIC on the right side interacting with multi-NH 2 -βCDs are detected. C) The representative m / z spectra of RAL shown by the green arrow, BIC by the purple arrow, RAL plus βCD, RAL plus RAM-βCD, and RAL plus HP-βCD by the red arrows, are detected by ESI-MS. The spectra of RAL plus βCD are mostly found by adding Na+ or NH 4 + to RAL plus βCD. The different m / z spectra of RAL plus RAM-βCD and RAL plus HP-βCD are shown because each RAM-βCD and HP-βCD contains a different number of side chains.

    Techniques Used: Produced, Binding Assay, Generated, Concentration Assay

    Estimated binding models of H-RAL to PFV intasome. A) INSTI-binding pocket shown in PFV intasome containing PFV integrase, viral DNA (3′ adenosine, A17), and divalent cations Mn 2+ (PDB ID, 3L2V). B) A best-fit model of H-RAL superimposed with RAL binding to the binding pocket of PFV-IN intasome. The 1,3,4-oxadiazole ring of RAL, but not H-RAL, fits into a hydrophobic cavity including Tyr 212 via a Π–Π interaction. C) Top 10 binding models of H-RAL interacting with the binding pocket generated by the docking simulation from the RAL-binding template of 3L2V. The carbons of PFV, RAL, H-RAL, and Mn 2+ are shown in tan, purple, hot pink, and plum colors, respectively. The viral DNA structure is shown in magenta and blue. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. Molecular graphics were created using UCSF Chimera. All docking simulations were performed with SeeSAR v12.1.
    Figure Legend Snippet: Estimated binding models of H-RAL to PFV intasome. A) INSTI-binding pocket shown in PFV intasome containing PFV integrase, viral DNA (3′ adenosine, A17), and divalent cations Mn 2+ (PDB ID, 3L2V). B) A best-fit model of H-RAL superimposed with RAL binding to the binding pocket of PFV-IN intasome. The 1,3,4-oxadiazole ring of RAL, but not H-RAL, fits into a hydrophobic cavity including Tyr 212 via a Π–Π interaction. C) Top 10 binding models of H-RAL interacting with the binding pocket generated by the docking simulation from the RAL-binding template of 3L2V. The carbons of PFV, RAL, H-RAL, and Mn 2+ are shown in tan, purple, hot pink, and plum colors, respectively. The viral DNA structure is shown in magenta and blue. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. Molecular graphics were created using UCSF Chimera. All docking simulations were performed with SeeSAR v12.1.

    Techniques Used: Binding Assay, Generated



    Similar Products

    seesar v12.1  (BioSolveIT GmbH)
    90
    BioSolveIT GmbH seesar v12.1
    Inclusion of RAL into CDs. A) The structure <t>of</t> <t>βCD</t> is used from the crystallography (PDB ID 3GCT). Those of RAM-βCD and HP-βCD are produced by the addition of side chains, 6-methyl and 6-hydroxypropyl groups, respectively, to the βCD, and representative binding models of RAL to βCD, RAM-βCD, and HP-βCD are generated by <t>SeeSAR.</t> Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. B) SPR illustrated the interaction of the drugs with multi-NH 2 -βCDs immobilized on a sensor chip. Sensorgrams of each concentration of RAL on the middle and BIC on the right side interacting with multi-NH 2 -βCDs are detected. C) The representative m / z spectra of RAL shown by the green arrow, BIC by the purple arrow, RAL plus βCD, RAL plus RAM-βCD, and RAL plus HP-βCD by the red arrows, are detected by ESI-MS. The spectra of RAL plus βCD are mostly found by adding Na+ or NH 4 + to RAL plus βCD. The different m / z spectra of RAL plus RAM-βCD and RAL plus HP-βCD are shown because each RAM-βCD and HP-βCD contains a different number of side chains.
    Seesar V12.1, supplied by BioSolveIT GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/seesar+v12%2E1/pmc10758923-160-36-38?v=BioSolveIT+GmbH
    Average 90 stars, based on 1 article reviews
    seesar v12.1 - by Bioz Stars, 2026-07
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Inclusion of RAL into CDs. A) The structure of βCD is used from the crystallography (PDB ID 3GCT). Those of RAM-βCD and HP-βCD are produced by the addition of side chains, 6-methyl and 6-hydroxypropyl groups, respectively, to the βCD, and representative binding models of RAL to βCD, RAM-βCD, and HP-βCD are generated by SeeSAR. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. B) SPR illustrated the interaction of the drugs with multi-NH 2 -βCDs immobilized on a sensor chip. Sensorgrams of each concentration of RAL on the middle and BIC on the right side interacting with multi-NH 2 -βCDs are detected. C) The representative m / z spectra of RAL shown by the green arrow, BIC by the purple arrow, RAL plus βCD, RAL plus RAM-βCD, and RAL plus HP-βCD by the red arrows, are detected by ESI-MS. The spectra of RAL plus βCD are mostly found by adding Na+ or NH 4 + to RAL plus βCD. The different m / z spectra of RAL plus RAM-βCD and RAL plus HP-βCD are shown because each RAM-βCD and HP-βCD contains a different number of side chains.

    Journal: PNAS Nexus

    Article Title: Conversion of raltegravir carrying a 1,3,4-oxadiazole ring to a hydrolysis product upon pH changes decreases its antiviral activity

    doi: 10.1093/pnasnexus/pgad446

    Figure Lengend Snippet: Inclusion of RAL into CDs. A) The structure of βCD is used from the crystallography (PDB ID 3GCT). Those of RAM-βCD and HP-βCD are produced by the addition of side chains, 6-methyl and 6-hydroxypropyl groups, respectively, to the βCD, and representative binding models of RAL to βCD, RAM-βCD, and HP-βCD are generated by SeeSAR. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. B) SPR illustrated the interaction of the drugs with multi-NH 2 -βCDs immobilized on a sensor chip. Sensorgrams of each concentration of RAL on the middle and BIC on the right side interacting with multi-NH 2 -βCDs are detected. C) The representative m / z spectra of RAL shown by the green arrow, BIC by the purple arrow, RAL plus βCD, RAL plus RAM-βCD, and RAL plus HP-βCD by the red arrows, are detected by ESI-MS. The spectra of RAL plus βCD are mostly found by adding Na+ or NH 4 + to RAL plus βCD. The different m / z spectra of RAL plus RAM-βCD and RAL plus HP-βCD are shown because each RAM-βCD and HP-βCD contains a different number of side chains.

    Article Snippet: The crystal structures of βCD (PDB accession number, 3CGT) were extracted from the RCSB Protein Data Bank ( http://www.rcsb.org ) and were used to produce the structures of βCD derivatives such as RAM-βCD and HP-βCD using SeeSAR v12.1 (BioSolveIT GmbH, Sankt Augustin, Germany).

    Techniques: Produced, Binding Assay, Generated, Concentration Assay

    Estimated binding models of H-RAL to PFV intasome. A) INSTI-binding pocket shown in PFV intasome containing PFV integrase, viral DNA (3′ adenosine, A17), and divalent cations Mn 2+ (PDB ID, 3L2V). B) A best-fit model of H-RAL superimposed with RAL binding to the binding pocket of PFV-IN intasome. The 1,3,4-oxadiazole ring of RAL, but not H-RAL, fits into a hydrophobic cavity including Tyr 212 via a Π–Π interaction. C) Top 10 binding models of H-RAL interacting with the binding pocket generated by the docking simulation from the RAL-binding template of 3L2V. The carbons of PFV, RAL, H-RAL, and Mn 2+ are shown in tan, purple, hot pink, and plum colors, respectively. The viral DNA structure is shown in magenta and blue. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. Molecular graphics were created using UCSF Chimera. All docking simulations were performed with SeeSAR v12.1.

    Journal: PNAS Nexus

    Article Title: Conversion of raltegravir carrying a 1,3,4-oxadiazole ring to a hydrolysis product upon pH changes decreases its antiviral activity

    doi: 10.1093/pnasnexus/pgad446

    Figure Lengend Snippet: Estimated binding models of H-RAL to PFV intasome. A) INSTI-binding pocket shown in PFV intasome containing PFV integrase, viral DNA (3′ adenosine, A17), and divalent cations Mn 2+ (PDB ID, 3L2V). B) A best-fit model of H-RAL superimposed with RAL binding to the binding pocket of PFV-IN intasome. The 1,3,4-oxadiazole ring of RAL, but not H-RAL, fits into a hydrophobic cavity including Tyr 212 via a Π–Π interaction. C) Top 10 binding models of H-RAL interacting with the binding pocket generated by the docking simulation from the RAL-binding template of 3L2V. The carbons of PFV, RAL, H-RAL, and Mn 2+ are shown in tan, purple, hot pink, and plum colors, respectively. The viral DNA structure is shown in magenta and blue. Nitrogen, oxygen, carbon, and fluorine atoms of the molecules are shown in blue, red, pale orange, and green colors, respectively. Molecular graphics were created using UCSF Chimera. All docking simulations were performed with SeeSAR v12.1.

    Article Snippet: The crystal structures of βCD (PDB accession number, 3CGT) were extracted from the RCSB Protein Data Bank ( http://www.rcsb.org ) and were used to produce the structures of βCD derivatives such as RAM-βCD and HP-βCD using SeeSAR v12.1 (BioSolveIT GmbH, Sankt Augustin, Germany).

    Techniques: Binding Assay, Generated