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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. Hockov, 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 :  2.26
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hypoxanthine-Guanine Phosphoribosyltransferase, Acyclic Nucleoside Monophosphonates, Malaria, 6-Oxopurine Phosphoribosyltransferase, 9- [(N-Phosphonoethyl-N-Phosphonoethoxyethyl)-2-Aminoethyl]-8- Bromoguanine, 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  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
13L34Ligand/Ion[(E)-2-(2-{[2-(2-AMINO-8-BROMO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ETHYL][(E)-2-PHOSPHONOETHENYL]AMINO}ETHOXY)ETHENYL]PHOSPHONIC ACID
2MG6Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP 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 , MG A:302 , PO4 A:303 , HOH A:411 , HOH A:422BINDING SITE FOR RESIDUE 3L3 A 301
02AC2SOFTWAREGLU A:133 , ASP A:134 , ILE A:135 , 3L3 A:301 , HOH A:430BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWARELEU A:67 , LYS A:68 , GLY A:69 , ASP A:193 , ARG A:199 , 3L3 A:301 , HOH A:429BINDING SITE FOR RESIDUE PO4 A 303
04AC4SOFTWAREILE B:135 , 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 , MG B:302 , PO4 B:304 , HOH B:409BINDING SITE FOR RESIDUE 3L3 B 301
05AC5SOFTWAREGLU B:133 , ASP B:134 , 3L3 B:301BINDING SITE FOR RESIDUE MG B 302
06AC6SOFTWARELYS B:68 , GLY B:69 , ASP B:193 , ARG B:199 , 3L3 B:301 , HOH B:420BINDING SITE FOR RESIDUE PO4 B 304
07AC7SOFTWAREILE 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 , MG C:302 , MG C:303 , PO4 C:304 , HOH C:415 , HOH C:421 , HOH C:429BINDING SITE FOR RESIDUE 3L3 C 301
08AC8SOFTWAREGLU C:133 , ASP C:134 , ILE C:135 , 3L3 C:301 , HOH C:419 , HOH C:420 , HOH C:429BINDING SITE FOR RESIDUE MG C 302
09AC9SOFTWAREASP C:193 , 3L3 C:301 , PO4 C:304 , HOH C:421BINDING SITE FOR RESIDUE MG C 303
10BC1SOFTWARELYS C:68 , GLY C:69 , ASP C:193 , ARG C:199 , 3L3 C:301 , MG C:303 , HOH C:419BINDING SITE FOR RESIDUE PO4 C 304
11BC2SOFTWAREASP 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 , LEU D:192 , ASP D:193 , PO4 D:304 , HOH D:412 , HOH D:429 , HOH D:444BINDING SITE FOR RESIDUE 3L3 D 301
12BC3SOFTWAREGLU D:133 , ASP D:134 , HOH D:429 , HOH D:430 , HOH D:431BINDING SITE FOR RESIDUE MG D 302
13BC4SOFTWAREASP D:193 , PO4 D:304BINDING SITE FOR RESIDUE MG D 303
14BC5SOFTWARELEU D:67 , LYS D:68 , GLY D:69 , ASP D:193 , ARG D:199 , 3L3 D:301 , MG D:303 , HOH D:430BINDING SITE FOR RESIDUE PO4 D 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Lys A:68
2Asp A:89 -Arg A:90
3Gly B:57 -Gly B:58
4Leu B:67 -Lys B:68
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 4RAB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RAB)

(-) 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..hhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rab A   5 PGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYK 216
                                    14        24        34        44        54        64        74        84        94       119       129       139       149       159       169       179       189       199       209       
                                                                                                                            103|                                                                                                 
                                                                                                                             119                                                                                                 


Chain B 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...eeeeee...hhhhhhhhhhhhhhhhh......eeeeeeee...ee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rab B   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSPMTVDFIRLKSKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83       |94       114       124       134       144       154       164     ||176       186       196       206       216 
                                                                                                                  91|       103|                                                     170|                                            
                                                                                                                   93        114                                                      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.......eeeeeeee...ee...hhhhh...eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rab C   5 PGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    14        24        34        44        54        64        74        84        94       114       124       134       144       154       164       174       184       194       204       214   
                                                                                                                           102|                                                                                                        
                                                                                                                            113                                                                                                        


Chain D 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...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee...ee..hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee.....................eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rab D   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       115       125       135       145       155       165       175       185       195       205       215  
                                                                                                                            102|                                                                                                      
                                                                                                                             115
   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 4RAB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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    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 ]  
 

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

(-) Related Entries Specified in the PDB File

4rac 4rad 4ran 4rao 4raq