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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 :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  6-Oxopurine Phosphoribosyltransferase, 9-[(N-Phosphonoethyl-N- Phosphonomethoxyethyl)-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, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
13L44Ligand/Ion[(2-{[2-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ETHYL][(E)-2-PHOSPHONOETHENYL]AMINO}ETHOXY)METHYL]PHOSPHONIC ACID
2MG7Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:67 , LYS A:68 , GLY A:69 , LEU A:101 , ASP 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 , LEU A:192 , ASP A:193 , ARG A:199 , MG A:302 , HOH A:401 , HOH A:402 , HOH A:403 , HOH A:410 , HOH A:411 , HOH A:416 , HOH A:420 , HOH A:433 , HOH A:435 , HOH A:438 , HOH A:456BINDING SITE FOR RESIDUE 3L4 A 301
02AC2SOFTWAREASP A:193 , 3L4 A:301 , HOH A:416 , HOH A:417 , HOH A:420 , HOH A:456BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREGLU A:133 , ASP A:134 , HOH A:401 , HOH A:402 , HOH A:406 , HOH A:408BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWARELEU B:67 , LYS B:68 , GLY B:69 , LEU B:101 , ASP 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 , LEU B:192 , ASP B:193 , ARG B:199 , MG B:302 , HOH B:402 , HOH B:403 , HOH B:413 , HOH B:416 , HOH B:419 , HOH B:439 , HOH B:446 , HOH B:457BINDING SITE FOR RESIDUE 3L4 B 301
05AC5SOFTWAREASP B:193 , 3L4 B:301 , HOH B:406 , HOH B:409 , HOH B:419 , HOH B:457BINDING SITE FOR RESIDUE MG B 302
06AC6SOFTWAREGLU B:133 , ASP B:134 , HOH B:402 , HOH B:434 , HOH B:446 , HOH B:448BINDING SITE FOR RESIDUE MG B 303
07AC7SOFTWARELEU C:67 , LYS C:68 , GLY C:69 , 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 , LEU C:192 , ASP C:193 , ARG C:199 , MG C:303 , HOH C:401 , HOH C:403 , HOH C:411 , HOH C:412 , HOH C:414 , HOH C:415 , HOH C:422 , HOH C:428 , HOH C:432 , HOH C:456BINDING SITE FOR RESIDUE 3L4 C 301
08AC8SOFTWAREGLU C:133 , ASP C:134 , HOH C:401 , HOH C:403 , HOH C:404 , HOH C:458BINDING SITE FOR RESIDUE MG C 302
09AC9SOFTWAREASP C:193 , 3L4 C:301 , HOH C:412 , HOH C:455 , HOH C:456 , HOH C:457BINDING SITE FOR RESIDUE MG C 303
10BC1SOFTWARELYS D:68 , GLY D:69 , ASP D:137 , THR D:138 , GLY D:139 , THR D:141 , LYS D:165 , LYS D:185 , PHE D:186 , VAL D:187 , ASP D:193 , ARG D:199 , HOH D:431 , HOH D:432BINDING SITE FOR RESIDUE 3L4 D 301
11BC2SOFTWAREGLU D:133 , ASP D:134 , HOH D:430 , HOH D:431 , HOH D:432BINDING SITE FOR RESIDUE MG D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Lys A:68
2Leu B:67 -Lys B:68
3Val B:171 -Gly B:172
4Leu C:67 -Lys C:68
5Gly C:118 -Asp C:119
6Leu D:67 -Lys D:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RAC)

(-) 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:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeeee...eehhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee.....................eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rac A   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       113       123       133       143       153       163       173       183       193       203       213    
                                                                                                                            102|                                                                                                        
                                                                                                                             113                                                                                                        


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...eeeeeee..hhhhhhhhhhhhhhhhh.....eeeeeeeee...eeehhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rac B   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSSIPMTVDFIRLKSDIKVIDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYK 216
                                    13        23        33        43        53        63        73        83    ||  95       113  ||   126       136       146       156       166       176       186       196       206       216
                                                                                                               88|         103| 116|                                                                                                
                                                                                                                91          112  120                                                                                                


Chain C from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeeeee..eee....hhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rac C   6 GVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    15        25        35        45        55        65        75        85        95      |114       124       134       144       154       164       174       184       194       204       214   
                                                                                                                          102|                                                                                                         
                                                                                                                           112                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.......ee.hhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee.......hhhhhh..eeeeeeeee..hhhhhhhhhhhh...eeeeeeeeee.........eeeeee.....................eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rac D   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRNPKMVKVASLLVKRRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       115       125       135       145    || 157       169       179       189       199       209        
                                                                                                                            102|                                150|          166|                                                
                                                                                                                             115                                 153           169
   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 4RAC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly C:118 - Asp C:119   [ RasMol ]  
    Leu A:67 - Lys A:68   [ RasMol ]  
    Leu B:67 - Lys B:68   [ RasMol ]  
    Leu C:67 - Lys C:68   [ RasMol ]  
    Leu D:67 - Lys D:68   [ RasMol ]  
    Val B:171 - Gly B:172   [ RasMol ]  
 

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  4rac
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  HPRT_HUMAN | P00492
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  2.4.2.8
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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 4rad 4ran 4rao 4raq 5brn 5bsk 5hia

(-) Related Entries Specified in the PDB File

4rab 4rad 4ran 4rao 4raq