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(-) Description

Title :  HDAC2 WITH LIGAND BRD4884
 
Authors :  S. Steinbacher
Date :  22 Mar 16  (Deposition) - 31 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hdac Histone Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. F. Wagner, M. Weiwer, S. Steinbacher, A. Schomburg, P. Reinemer, J. P. Gale, A. J. Campbell, S. L. Fisher, W. N. Zhao, S. A. Reis, K. M. Hennig, M. Thomas, P. Muller, M. R. Jefson, D. M. Fass, S. J. Haggarty, Y. L. Zhang, E. B. Holson
Kinetic And Structural Insights Into The Binding Of Histone Deacetylase 1 And 2 (Hdac1, 2) Inhibitors.
Bioorg. Med. Chem. V. 24 4008 2016
PubMed-ID: 27377864  |  Reference-DOI: 10.1016/J.BMC.2016.06.040

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 2
    ChainsA, B, C
    EC Number3.5.1.98
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneHDAC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHD2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 21)

Asymmetric Unit (7, 21)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2IWX3Ligand/IonN-(4-AMINO-4'-FLUORO[1,1'-BIPHENYL]-3-YL)OXANE-4-CARBOXAMIDE
3PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PG51Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
6PGE2Ligand/IonTRIETHYLENE GLYCOL
7ZN3Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IWX1Ligand/IonN-(4-AMINO-4'-FLUORO[1,1'-BIPHENYL]-3-YL)OXANE-4-CARBOXAMIDE
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5PG51Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
6PGE2Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IWX1Ligand/IonN-(4-AMINO-4'-FLUORO[1,1'-BIPHENYL]-3-YL)OXANE-4-CARBOXAMIDE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PG5-1Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IWX1Ligand/IonN-(4-AMINO-4'-FLUORO[1,1'-BIPHENYL]-3-YL)OXANE-4-CARBOXAMIDE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5PG5-1Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:181 , HIS A:183 , ASP A:269 , IWX A:403binding site for residue ZN A 401
02AC2SOFTWAREASP A:179 , ASP A:181 , HIS A:183 , SER A:202 , PHE A:203binding site for residue CA A 402
03AC3SOFTWARETYR A:29 , MET A:35 , ARG A:39 , PHE A:114 , GLY A:143 , LEU A:144 , HIS A:145 , HIS A:146 , GLY A:154 , PHE A:155 , CYS A:156 , ASP A:181 , HIS A:183 , ASP A:269 , LEU A:276 , GLY A:305 , GLY A:306 , TYR A:308 , ZN A:401 , HOH A:606binding site for residue IWX A 403
04AC4SOFTWAREPHE A:192 , THR A:195 , VAL A:198 , TYR A:227 , HOH A:562 , HOH A:583binding site for residue CA A 404
05AC5SOFTWAREARG A:311 , GLY A:343 , HOH A:630binding site for residue PG5 A 405
06AC6SOFTWAREASN A:26 , TYR A:27 , GLY A:110binding site for residue PGE A 406
07AC7SOFTWARELYS A:71 , ALA A:191binding site for residue PGE A 407
08AC8SOFTWAREASP B:181 , HIS B:183 , ASP B:269 , IWX B:403binding site for residue ZN B 401
09AC9SOFTWAREASP B:179 , ASP B:181 , HIS B:183 , SER B:202 , PHE B:203binding site for residue CA B 402
10AD1SOFTWARETYR B:29 , MET B:35 , ARG B:39 , PHE B:114 , GLY B:143 , LEU B:144 , HIS B:145 , HIS B:146 , GLY B:154 , PHE B:155 , CYS B:156 , ASP B:181 , HIS B:183 , PHE B:210 , ASP B:269 , GLY B:305 , GLY B:306 , TYR B:308 , ZN B:401 , HOH B:602binding site for residue IWX B 403
11AD2SOFTWAREPHE B:192 , THR B:195 , VAL B:198 , TYR B:227 , HOH B:585 , HOH B:590binding site for residue CA B 404
12AD3SOFTWARELYS B:284 , HIS B:349 , HOH B:512 , HOH B:513 , GLU C:67 , THR C:70binding site for residue PEG B 405
13AD4SOFTWAREASN B:26 , TYR B:27 , ASP B:109binding site for residue PEG B 406
14AD5SOFTWAREGLU B:340 , GLY B:343binding site for residue PEG B 407
15AD6SOFTWAREASN B:354 , LEU C:169 , TYR C:171 , GLN C:173 , ARG C:197binding site for residue PG4 B 408
16AD7SOFTWAREASP C:181 , HIS C:183 , ASP C:269 , IWX C:403binding site for residue ZN C 401
17AD8SOFTWAREASP C:179 , ASP C:181 , HIS C:183 , SER C:202 , PHE C:203binding site for residue CA C 402
18AD9SOFTWARETYR C:29 , MET C:35 , ARG C:39 , PHE C:114 , GLY C:143 , LEU C:144 , HIS C:145 , HIS C:146 , GLY C:154 , PHE C:155 , CYS C:156 , ASP C:181 , HIS C:183 , PHE C:210 , ASP C:269 , LEU C:276 , GLY C:305 , GLY C:306 , TYR C:308 , ZN C:401 , HOH C:516 , HOH C:617binding site for residue IWX C 403
19AE1SOFTWAREPHE C:192 , THR C:195 , VAL C:198 , TYR C:227 , HOH C:555 , HOH C:570binding site for residue CA C 404
20AE2SOFTWAREASP C:23 , ASN C:26 , TYR C:27binding site for residue PEG C 405
21AE3SOFTWAREPRO B:344 , HOH C:564 , HOH C:646binding site for residue PEG C 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:210 -Pro A:211
2Gly A:343 -Pro A:344
3Phe B:210 -Pro B:211
4Gly B:343 -Pro B:344
5Phe C:210 -Pro C:211
6Gly C:343 -Pro C:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IWG)

(-) 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:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhh.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iwg A  12 GKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLP 379
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371        

Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...hhhhh.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iwg B  14 KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLP 379
                                    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      

Chain C from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...hhhhh.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iwg C  14 KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLP 379
                                    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      

   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 5IWG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (78, 78)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        HDAC2_HUMAN | Q927693max 4lxz 4ly1 5ix0

(-) Related Entries Specified in the PDB File

5ix0