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(-) Description

Title :  AZA-ACYCLIC NUCLEOSIDE PHOSPHONATES CONTAINING A SECOND PHOSPHONATE GROUP AS INHIBITORS OF THE HUMAN, PLASMODIUM FALCIPARUM AND VIVAX 6-OXOPURINE PHOSPHORIBOSYLTRANSFERASES AND THEIR PRO-DRUGS AS ANTIMALARIAL AGENTS
 
Authors :  D. T. Keough, D. Hockova, Z. Janeba, T. -H. Wang, L. Naesens, M. D. Edstei M. Chavchich, L. W. Guddat
Date :  10 Sep 14  (Deposition) - 07 Jan 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  6-Oxopurine Phosphoribosyltransferase, 9-[(N-(2-Cyanoethyl)-N-(2- Phosphonoethyl))-2-Aminoethyl]-Guanine, Cytoplasmic, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Keough, D. Hockova, Z. Janeba, T. H. Wang, L. Naesens, M. D. Edstein, M. Chavchich, L. W. Guddat
Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors Of The Human, Plasmodium Falciparum And Vivax 6-Oxopurine Phosphoribosyltransferases And Their Prodrugs As Antimalarial Agents.
J. Med. Chem. V. 58 827 2015
PubMed-ID: 25494538  |  Reference-DOI: 10.1021/JM501416T

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HPRT1, HPRT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGPRT, HGPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
13L64Ligand/Ion(2-{[2-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ETHYL](3-AMINOPROPYL)AMINO}ETHYL)PHOSPHONIC ACID
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:137 , THR A:138 , GLY A:139 , LYS A:140 , THR A:141 , LYS A:165 , LYS A:185 , PHE A:186 , VAL A:187 , ASP A:193 , HOH A:401 , HOH A:404 , HOH A:405BINDING SITE FOR RESIDUE 3L6 A 301
2AC2SOFTWAREGLU A:133 , ASP A:134 , HOH A:406 , HOH A:407 , HOH A:408BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASP B:137 , THR B:138 , GLY B:139 , LYS B:140 , THR B:141 , LYS B:165 , LYS B:185 , PHE B:186 , VAL B:187 , ASP B:193BINDING SITE FOR RESIDUE 3L6 B 301
4AC4SOFTWAREGLU B:133 , ASP B:134 , HOH B:404 , HOH B:405BINDING SITE FOR RESIDUE MG B 302
5AC5SOFTWARELEU C:101 , ILE C:135 , ASP C:137 , THR C:138 , GLY C:139 , LYS C:140 , THR C:141 , LYS C:165 , LYS C:185 , PHE C:186 , VAL C:187 , ASP C:193BINDING SITE FOR RESIDUE 3L6 C 301
6AC6SOFTWAREGLU C:133 , ASP C:134 , HOH C:402BINDING SITE FOR RESIDUE MG C 302
7AC7SOFTWARELEU D:101 , ILE D:135 , ASP D:137 , THR D:138 , GLY D:139 , LYS D:140 , THR D:141 , LYS D:165 , LYS D:185 , PHE D:186 , VAL D:187 , ASP D:193 , MG D:302BINDING SITE FOR RESIDUE 3L6 D 301
8AC8SOFTWAREGLU D:133 , ASP D:134 , 3L6 D:301BINDING SITE FOR RESIDUE MG D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Lys A:68
2Gly A:118 -Asp A:119
3Leu B:67 -Lys B:68
4Leu C:67 -Lys C:68
5Arg C:100 -Leu C:101
6Leu D:67 -Lys D:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RAN)

(-) 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:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee.............eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ran A   3 RSPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKVIGGDSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    12        22        32        42        52        62        72        82        92       102|   || 126       136       146       156       166       176       186       196       206       216 
                                                                                                                             102| 119|                                                                                               
                                                                                                                              115  122                                                                                               


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.......eeeeee.....hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ran B   3 RSPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    12        22        32        42        52        62        72        82        92       117       127       137       147       157       167       177       187       197       207       217
                                                                                                                           100|                                                                                                     
                                                                                                                            116                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.......eeeeee........hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ran C   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       115       125       135       145       155       165       175       185       195       205       215  
                                                                                                                           101|                                                                                                       
                                                                                                                            114                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ran D   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLVIGGLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       116 ||    131       141       151       161       171       181       191       201       211      
                                                                                                                           101|  ||                                                                                             
                                                                                                                            115  ||                                                                                             
                                                                                                                               118|                                                                                             
                                                                                                                                124
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4RAN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPRT_HUMAN | P00492: 1bzy 1d6n 1hmp 1z7g 2vfa 3gep 3ggc 3ggj 4ijq 4kn6 4rab 4rac 4rad 4rao 4raq 5brn 5bsk 5hia

(-) Related Entries Specified in the PDB File

4rab 4rac 4rad 4rao 4raq