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(-) Description

Title :  GS-8374, A NOVEL PHOSPHONATE-CONTAINING INHIBITOR OF HIV-1 PROTEASE, EFFECTIVELY INHIBITS HIV PR MUTANTS WITH AMINO ACID INSERTIONS
 
Authors :  K. Grantz Saskova, J. Brynda, P. Rezacova, M. Kozisek, J. Konvalinka
Date :  14 Aug 13  (Deposition) - 07 May 14  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1 Protease, Aspartic Protease, Amino Acid Insertion, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Grantz Saskova, M. Kozisek, K. Stray, D. De Jong, P. Rezaova, J. Brynda, N. M. Van Maarseveen, M. Nijhuis, T. Cihlar, J. Konvalinka
Gs-8374, A Prototype Phosphonate-Containing Inhibitor Of Hiv-1 Protease, Effectively Inhibits Protease Mutants With Amino Acid Insertions.
J. Virol. V. 88 3586 2014
PubMed-ID: 24371077  |  Reference-DOI: 10.1128/JVI.02688-13

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: POL
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1KGQ2Ligand/IonDIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ASP A:29 , ASP A:30 , ILE A:32 , GLY A:49 , GLY A:50 , ILE A:51 , PHE A:54 , HOH A:309 , HOH A:318 , HOH A:341 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , VAL B:47 , VAL B:48 , GLY B:49 , GLY B:50 , PHE B:54 , PRO B:82 , ILE B:85BINDING SITE FOR RESIDUE KGQ A 201
2AC2SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:30 , VAL A:48 , GLY A:49 , GLY A:50 , PRO A:82 , ILE A:85 , HOH A:309 , HOH A:345 , ASP B:25 , GLY B:27 , ASP B:29 , ASP B:30 , ILE B:32 , GLY B:49 , GLY B:50 , ILE B:51 , PHE B:54BINDING SITE FOR RESIDUE KGQ A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M8Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4M8Y)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eee..........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4m8y A   1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
                                    10        20        30        40        50        60        70        80        90       100


Chain B from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee..........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4m8y B   1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
                                    10        20        30        40        50        60        70        80        90       100
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4M8Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M8Y)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  4m8y
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q90JJ9_9HIV1 | Q90JJ9: 4m8x

(-) Related Entries Specified in the PDB File

2rkf 2rkg 4m8x