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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. Edstein M. Chavchich, L. W. Guddat
Date :  10 Sep 14  (Deposition) - 07 Jan 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  6-Oxopurine Phosphoribosyltransferase, 9-[(N-Phosphonoethyl-N- Phosphonoethoxyethyl)-2-Aminoethyl]Hypoxanthine, 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, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
13L74Ligand/Ion(2-{[2-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ETHYL](2-{[(E)-2-PHOSPHONOETHENYL]OXY}ETHYL)AMINO}ETHYL)PHOSPHONICACID
2MG8Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:68 , GLY A:69 , 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 , ASP A:193 , ARG A:199 , MG A:303 , HOH A:412 , HOH A:418 , HOH A:426 , HOH A:450 , HOH A:452BINDING SITE FOR RESIDUE 3L7 A 301
02AC2SOFTWAREGLU A:133 , ASP A:134 , HOH A:418 , HOH A:426 , HOH A:449 , HOH A:450BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREASP A:193 , 3L7 A:301 , HOH A:451 , HOH A:452BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWARELYS B:68 , GLY B:69 , GLU B:133 , 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 , ASP B:193 , ARG B:199 , MG B:302 , MG B:303 , HOH B:401 , HOH B:414 , HOH B:430 , HOH B:446 , HOH B:447 , HOH B:448BINDING SITE FOR RESIDUE 3L7 B 301
05AC5SOFTWAREGLU B:133 , ASP B:134 , 3L7 B:301BINDING SITE FOR RESIDUE MG B 302
06AC6SOFTWAREASP B:193 , 3L7 B:301 , HOH B:421 , HOH B:446 , HOH B:447 , HOH B:448BINDING SITE FOR RESIDUE MG B 303
07AC7SOFTWARELYS C:68 , GLY C:69 , ARG C:100 , 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:193 , ARG C:199 , MG C:303 , HOH C:402 , HOH C:405 , HOH C:411 , HOH C:413 , HOH C:418 , HOH C:421 , HOH C:449 , HOH C:450 , HOH C:451 , HOH C:453BINDING SITE FOR RESIDUE 3L7 C 301
08AC8SOFTWAREGLU C:133 , ASP C:134 , HOH C:405 , HOH C:411 , HOH C:448 , HOH C:450 , HOH C:451BINDING SITE FOR RESIDUE MG C 302
09AC9SOFTWAREASP C:193 , 3L7 C:301 , HOH C:412 , HOH C:421 , HOH C:438 , HOH C:452 , HOH C:453BINDING SITE FOR RESIDUE MG C 303
10BC1SOFTWARELYS D:68 , GLY D:69 , 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 , ARG D:199 , MG D:303 , HOH D:401 , HOH D:405 , HOH D:410 , HOH D:432 , HOH D:445BINDING SITE FOR RESIDUE 3L7 D 301
11BC2SOFTWAREGLU D:133 , ASP D:134 , HOH D:401 , HOH D:410 , HOH D:445 , HOH D:447BINDING SITE FOR RESIDUE MG D 302
12BC3SOFTWAREASP D:193 , 3L7 D:301 , HOH D:425 , HOH D:446BINDING SITE FOR RESIDUE MG D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Lys A:68
2Gly B:57 -Gly B:58
3Leu B:67 -Lys B:68
4Ile B:92 -Pro B:93
5Leu C:67 -Lys C:68
6Leu D:67 -Lys D:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RAO)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rao A   1 ATRSPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSRSIPMTVDFIRLKLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYK 216
                                    10        20        30        40        50        60        70        80       |91       101||     129       139       149       159       169       179       189       199       209       
                                                                                                                  88|         102|                                                                                               
                                                                                                                   90          121                                                                                               


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeee...ee........eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee.........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rao B   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKVIGGDDTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       115    || 127       137       147       157       167  ||   179       189       199       209        
                                                                                                                            102|  120|                                            170|                                            
                                                                                                                             115   123                                             173                                            


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..hhhhhhhhhhhhhhhhh.......eeeeeee........hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rao C   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       114       124       134       144       154       164       174       184       194       204       214   
                                                                                                                            102|                                                                                                       
                                                                                                                             114                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.......eeeeeeeee....eee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rao D   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSYDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       103||     120       130       140       150       160       170       180       190       200       210       
                                                                                                                              104|                                                                                                         
                                                                                                                               112
   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 4RAO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  4rao
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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 4rac 4rad 4ran 4raq 5brn 5bsk 5hia

(-) Related Entries Specified in the PDB File

4rab 4rac 4rad 4ran 4raq