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(-) Description

Title :  HIV-1 WILD TYPE PROTEASE WITH GRL-0518A , AN ISOPHTHALAMIDE-DERIVED P2-P3 LIGAND WITH THE PARA-HYDOXYMETHYL SULFONAMIDE ISOSTERE AS THE P2' GROUP
 
Authors :  Y. -F. Wang, J. Agniswamy, I. T. Weber
Date :  05 Feb 17  (Deposition) - 10 May 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.27
Chains :  Asym./Biol. Unit :  A,B
Keywords :  An Isophthalamide-Derived P2-P3 Ligand, Hiv-1 Protease Inhibitor Grl- 0518A, Darunavir, Multidrug-Resistant, Hydrolase Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Ghosh, M. Brindisi, P. R. Nyalapatla, J. Takayama, J. R. Ella-Menye, S. Yashchuk, J. Agniswamy, Y. F. Wang, M. Aoki, M. Amano, I. T. Weber, H. Mitsuya
Design Of Novel Hiv-1 Protease Inhibitors Incorporating Isophthalamide-Derived P2-P3 Ligands: Synthesis, Biological Evaluation And X-Ray Structural Studies Of Inhibitor-Hiv-1 Protease Complex.
Bioorg. Med. Chem. 2017
PubMed-ID: 28434781  |  Reference-DOI: 10.1016/J.BMC.2017.04.005

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
18HD1Ligand/IonN~3~-{(2S,3R)-3-HYDROXY-4-[{[4-(HYDROXYMETHYL)PHENYL]SULFONYL}(2-METHYLPROPYL)AMINO]-1-PHENYLBUTAN-2-YL}-N~1~-METHYL-N~1~-[(4-METHYL-1,3-OXAZOL-2-YL)METHYL]BENZENE-1,3-DICARBOXAMIDE
2CL3Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , LEU A:23 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , VAL A:32 , GLY A:48 , GLY A:49 , VAL A:82 , ILE A:84 , HOH A:302 , HOH A:333 , HOH A:348 , HOH A:375 , ASP B:25 , GLY B:27 , ASP B:29 , ASP B:30 , GLY B:48 , GLY B:49 , ILE B:50 , ILE B:84 , HOH B:251binding site for residue 8HD A 201
2AC2SOFTWAREASP A:60 , HOH A:322 , HOH A:355 , HOH A:371 , HOH A:373 , HOH A:395binding site for residue NA A 202
3AC3SOFTWARETHR A:74 , ASN A:88 , HOH A:324 , HOH A:417 , ARG B:41binding site for residue CL A 203
4AC4SOFTWARELYS A:45 , MET A:46 , HOH A:317 , HOH A:329 , GLN B:92 , CL B:103 , HOH B:237binding site for residue GOL A 204
5AC5SOFTWAREASP B:60 , HOH B:217 , HOH B:224 , HOH B:281 , HOH B:313binding site for residue NA B 101
6AC6SOFTWARETRP B:6binding site for residue CL B 102
7AC7SOFTWAREGOL A:204 , THR B:74 , ASN B:88 , HOH B:231binding site for residue CL B 103
8AC8SOFTWARELEU A:5 , HOH A:319 , HOH A:328 , THR B:91 , ALA B:95 , HOH B:247binding site for residue GOL B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UPZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UPZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  5upz A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  5upz B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90
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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 5UPZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UPZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UPZ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        C8B467_9HIV1 | C8B467: 5ivt 5jfp 5jfu 5jg1 5ult 5uov

(-) Related Entries Specified in the PDB File

5ult 5uov