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(-) Description

Title :  POTENT, SELECTIVE AND CNS-PENETRANT TETRASUBSTITUTED CYCLOPROPANE CLASS IIA HISTONE DEACETYLASE (HDAC) INHIBITORS
 
Authors :  C. A. Luckhurst, P. Breccia, A. J. Stott, O. Aziz, H. Birch, R. W. Burli, S R. E. Jarvis, M. Lamers, P. Leonard, K. L. Matthews, G. Mcallister, S. P E. Saville-Stones, G. Wishart, D. Yates, C. Dominguez
Date :  22 May 15  (Deposition) - 10 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Class Iia Hdac Inhibitors, Hydroxamic Acid, Cns Exposure, Tetrasubstituted Cyclopropane, Cyclopropanation, Huntington'S Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Luckhurst, P. Breccia, A. J. Stott, O. Aziz, H. L. Birch, R. W. Burli, S. J. Hughes, R. E. Jarvis, M. Lamers, P. M. Leonard, K. L. Matthews, G. Mcallister, S. Pollack, E. Saville-Stones, G. Wishart, D. Yates, C. Dominguez
Potent, Selective, And Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors.
Acs Med. Chem. Lett. V. 7 34 2016
PubMed-ID: 26819662  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00302

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 4
    Chains: A, B
    EC Number: 3.5.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: HISTONE DEACETYLASE DOMAIN, RESIDUES 648-1033
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD4

 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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2OTF2Ligand/Ion(1S,2S,3S)-1-FLUORANYL-2-[4-(5-FLUORANYLPYRIMIDIN-2-YL)PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2OTF1Ligand/Ion(1S,2S,3S)-1-FLUORANYL-2-[4-(5-FLUORANYLPYRIMIDIN-2-YL)PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2OTF1Ligand/Ion(1S,2S,3S)-1-FLUORANYL-2-[4-(5-FLUORANYLPYRIMIDIN-2-YL)PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREZN A:2 , GLU A:677 , ARG A:681 , GLY A:696 , HIS A:802 , HIS A:803 , GLY A:811 , PHE A:812 , ASP A:840 , HIS A:842 , PHE A:871 , ASP A:934 , GLY A:975BINDING SITE FOR RESIDUE OTF A 1
2AC2SOFTWAREOTF A:1 , ASP A:840 , HIS A:842 , ASP A:934BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARECYS A:667 , CYS A:669 , HIS A:675 , CYS A:751BINDING SITE FOR RESIDUE ZN A 3
4AC4SOFTWAREASP A:838 , ASP A:840 , HIS A:842 , SER A:861 , LEU A:862BINDING SITE FOR RESIDUE NA A 4
5AC5SOFTWAREZN B:2 , HIS B:802 , HIS B:803 , PHE B:812 , ASP B:840 , HIS B:842 , PHE B:871 , ASP B:934 , GLY B:975 , HOH B:2001BINDING SITE FOR RESIDUE OTF B 1
6AC6SOFTWAREOTF B:1 , ASP B:840 , HIS B:842 , ASP B:934BINDING SITE FOR RESIDUE ZN B 2
7AC7SOFTWARECYS B:667 , CYS B:669 , HIS B:675 , CYS B:751BINDING SITE FOR RESIDUE ZN B 3
8AC8SOFTWAREASP B:838 , ASP B:840 , HIS B:842 , SER B:861 , LEU B:862BINDING SITE FOR RESIDUE NA B 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A2S)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Arg A:798 -Pro A:799
2Phe A:871 -Pro A:872
3Asp A:899 -Pro A:900
4Thr A:941 -Pro A:942
5Arg B:798 -Pro B:799
6Phe B:871 -Pro B:872
7Asp B:899 -Pro B:900
8Thr B:941 -Pro B:942

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A2S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A2S)

(-) Exons   (0, 0)

(no "Exon" information available for 5A2S)

(-) 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:380
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhh.....hhhhh...hhhhhhhhhhhhhh.hhhhheee.....hhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhh.ee.....ee..........hhhhhhhhhhhhhhhhhhhhhh....eeee....................hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh....eeeeeeee.................hhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeee...................hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a2s A  653 TTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPANRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQ 1032
                                   662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032


Chain B from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhh.............hhhhhhhhhhhhh..hhhhhee......hhhhhh...hhhhhhhh..hhhhhhhhh............ee.....ee..........hhhhhhhhhhhhhhhhhhhhhh.....eee....................hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh....eeeeeeee.................hhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a2s B  653 TTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPANRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQ 1032
                                   662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032
   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 5A2S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A2S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A2S)

(-) Gene Ontology  (74, 74)

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        HDAC4_HUMAN | P56524: 2h8n 2o94 2vqj 2vqm 2vqo 2vqq 2vqv 2vqw 3uxg 3uzd 3v31 4cbt 4cby

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