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(-) Description

Title :  BTGH84 IN COMPLEX WITH NH-BUTYLTHIAZOLINE
 
Authors :  Y. He, G. J. Davies
Date :  10 Jun 08  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase, Complex, Hydrolase, Inhibitor, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. A. Yuzwa, M. S. Macauley, J. E. Heinonen, X. Shan, R. J. Dennis, Y. He, G. E. Whitworth, K. A. Stubbs, E. J. Mceachern, G. J. Davies, D. J. Vocadlo
A Potent Mechanism-Inspired O-Glcnacase Inhibitor That Blocks Phosphorylation Of Tau In Vivo.
Nat. Chem. Biol. V. 4 483 2008
PubMed-ID: 18587388  |  Reference-DOI: 10.1038/NCHEMBIO.96

(-) Compounds

Molecule 1 - O-GLCNACASE BT_4395
    Atcc29148
    ChainsA, B
    EC Number3.2.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidYSBLLICPET28
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificBACTEROIDES THETAIOTAOMICRON
    Organism Taxid226186
    StrainVPI-5482
    SynonymBETA-HEXOSAMINIDASE, N-ACETYL-BETA- GLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, HEXOSAMINIDASE B, GH84, BTGH84

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NH41Ligand/IonAMMONIUM ION
3NHT2Ligand/Ion(3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NH41Ligand/IonAMMONIUM ION
3NHT1Ligand/Ion(3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2NH4-1Ligand/IonAMMONIUM ION
3NHT1Ligand/Ion(3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:137 , ASP A:344 , TYR A:345 , ARG A:347 , GLN A:551 , HOH A:2547 , HOH A:2548BINDING SITE FOR RESIDUE GOL A 1716
2AC2SOFTWAREGLU A:32 , GLU A:61 , ASP A:64BINDING SITE FOR RESIDUE NH4 A 1717
3AC3SOFTWAREGLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , CYS B:278 , TYR B:282 , THR B:310 , TRP B:337 , ASN B:339 , ASP B:344 , TYR B:345 , ASN B:372 , HOH B:2571BINDING SITE FOR RESIDUE NHT B 1716
4AC4SOFTWAREGLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , CYS A:278 , TYR A:282 , THR A:310 , TRP A:337 , ASN A:339 , ASP A:344 , TYR A:345 , ASN A:372 , HOH A:2549BINDING SITE FOR RESIDUE NHT A 1718

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VVN)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gln A:6 -Pro A:7
2Ala A:173 -Pro A:174
3Phe A:340 -Pro A:341
4Gln B:6 -Pro B:7
5Ala B:173 -Pro B:174
6Phe B:340 -Pro B:341

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VVN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VVN)

(-) Exons   (0, 0)

(no "Exon" information available for 2VVN)

(-) Sequences/Alignments

Asymmetric 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:648
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:712
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734  
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFGKDAPCTWGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNVSDEEQQVYLRQFVLTIEK 736
               SCOP domains d2vvna3 A:4-126 Glucosaminidase GH84, N-terminal domain                                                                    d2vvna2 A:127-436 Glucosaminidase GH84, catalytic domain                                                                                                                                                                                                                                                              d2vvna1 A:437-589 Glucosaminidase GH84 post-catalytic domain                                                                                             ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeee.....hhhhhhhhhhhh...ee....eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee.............hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh..............---------..eeee..eeee..------------.eeeeeeeeeeeeeee..------------------------------.eeee....eeeeee.-------------.eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvn A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKM---------LPLQVKANRVLISP------------VEIELDAIYPGENIQINF------------------------------RLSAGLQKAPVKFVRF-------------QFVLTIEK 715
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593 |       - |     613    |    -       633       643    |    -         -         -     | 683       693|        -    |  713  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         595       605          618          631              648                            679            694           708       

Chain B from PDB  Type:PROTEIN  Length:648
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:712
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734  
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFGKDAPCTWGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNVSDEEQQVYLRQFVLTIEK 736
               SCOP domains d2vvnb3 B:4-126 Glucosaminidase GH84, N-terminal domain                                                                    d2vvnb2 B:127-436 Glucosaminidase GH84, catalytic domain                                                                                                                                                                                                                                                              d2vvnb1 B:437-589 Glucosaminidase GH84 post-catalytic domain                                                                                             ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------Glyco_hydro_20b-2vvnB03 B:65-125                             ----NAGidase-2vvnB01 B:130-425                                                                                                                                                                                                                                                                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------Glyco_hydro_20b-2vvnB04 B:65-125                             ----NAGidase-2vvnB02 B:130-425                                                                                                                                                                                                                                                                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeeeeeeee...eeeee.....hhhhhhhhhhhh...ee....eeeeeee.....hhhhhhhh......eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh...............--------...eeee..eeee..------------.eeeeeeeeeeeeeee..------------------------------.eeee....eeeeee.--------------.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvn B   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKM--------NLPLQVKANRVLISP------------VEIELDAIYPGENIQINF------------------------------RLSAGLQKAPVKFVRF--------------FVLTIEK 715
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593 |       -|      613    |    -       633       643    |    -         -         -     | 683       693|        -     | 713  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         595      604           618          631              648                            679            694            709      

   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  (3, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VVN)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (OGA_BACTN | Q89ZI2)
molecular function
    GO:0016231    beta-N-acetylglucosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006517    protein deglycosylation    The removal of sugar residues from a glycosylated protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_BACTN | Q89ZI22chn 2cho 2j47 2j4g 2jiw 2vvs 2w4x 2w66 2w67 2wca 2wzh 2wzi 2x0h 2xj7 2xm1 2xm2 4ais 4aiu 4ur9 5abe 5abf 5abg 5abh 5fky 5fl0 5fl1

(-) Related Entries Specified in the PDB File

2chn BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY
2cho BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY
2j47 BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH A IMIDAZOLE-PUGNAC HYBRID INHIBITOR
2j4g BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH N-BUTYL-THIAZOLINE INHIBITOR
2jiw BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH 2-ACETYLAMINO-2-DEOXY-1- EPIVALIENAMINE