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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SIRT2 IN COMPLEX WITH A BROMINATED 2ND GENERATION SIRREAL INHIBITOR AND NAD+
 
Authors :  T. Rumpf, S. Gerhardt, O. Einsle, M. Jung
Date :  24 Sep 15  (Deposition) - 13 Jan 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Hydrolase, Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schiedel, T. Rumpf, B. Karaman, A. Lehotzky, J. Olah, S. Gerhardt, J. Ovadi, W. Sippl, O. Einsle, M. Jung
Aminothiazoles As Potent And Selective Sirt2 Inhibitors: A Structure-Activity Relationship Study.
J. Med. Chem. V. 59 1599 2016
PubMed-ID: 26696402  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01517

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET15B
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS RIPL
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 56-356
    Gene: SIRT2, SIR2L, SIR2L2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG 2,SIR2-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
15GN1Ligand/IonN-{5-[(7-BROMONAPHTHALEN-1-YL)METHYL]-1,3-THIAZOL-2-YL}-2-[(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYL]ACETAMIDE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
15GN2Ligand/IonN-{5-[(7-BROMONAPHTHALEN-1-YL)METHYL]-1,3-THIAZOL-2-YL}-2-[(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYL]ACETAMIDE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
15GN1Ligand/IonN-{5-[(7-BROMONAPHTHALEN-1-YL)METHYL]-1,3-THIAZOL-2-YL}-2-[(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYL]ACETAMIDE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 401
2AC2SOFTWAREPHE A:96 , ILE A:118 , PHE A:119 , PHE A:131 , ALA A:135 , TYR A:139 , PRO A:140 , ILE A:169 , ASP A:170 , PHE A:190 , ILE A:232 , VAL A:233 , PHE A:234 , MET A:299 , NAD A:403 , HOH A:549binding site for residue 5GN A 402
3AC3SOFTWAREGLY A:84 , ALA A:85 , GLY A:86 , THR A:89 , ILE A:93 , PRO A:94 , ASP A:95 , ARG A:97 , GLN A:167 , ASN A:168 , ILE A:169 , ASP A:170 , HIS A:187 , GLY A:261 , THR A:262 , SER A:263 , ASN A:286 , LYS A:287 , GLU A:288 , MET A:299 , GLY A:322 , GLU A:323 , CYS A:324 , 5GN A:402 , HOH A:510 , HOH A:514 , HOH A:534 , HOH A:535 , HOH A:551 , HOH A:562 , HOH A:644binding site for residue NAD A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DY4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DY4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DY4)

(-) Exons   (0, 0)

(no "Exon" information available for 5DY4)

(-) 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:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh.....eeeee.hhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhh.....eeeee.............hhhhh............eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dy4 A  53 GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS 356
                                    62        72        82        92     ||105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355 
                                                                        98|                                                                                                                                                                                                                                                              
                                                                        102
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  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 5DY4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DY4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DY4)

(-) Gene Ontology  (117, 117)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6l 4y6o 4y6q 5d7o 5d7p 5d7q 5dy5 5fyq 5g4c 5mar 5mat

(-) Related Entries Specified in the PDB File

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