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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH CCT363901
 
Authors :  V. Srikannathasan, L. B. Yann-Vai, R. Nowak, C. Johansson, C. Gileadi, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, P. Brennan, K. U. Oppermann
Date :  02 Dec 15  (Deposition) - 20 Jan 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Lysine-Specific Demethylase 5B (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Bavetsias, R. M. Lanigan, G. F. Ruda, B. Atrash, M. G. Mclaughlin, A. Tumber, N. Y. Mok, Y. Le Bihan, S. Dempster, K. J. Boxall, F. Jeganathan, S. B. Hatch, P. Savitsky, S. Velupillai, T. Krojer, K. S. England, J. Sejberg, C. Thai, A. Donovan, A. Pal, G. Scozzafava, J. M. Bennett, A. Kawamura, C. Johansson, A. Szykowska, C. Gileadi, N. A. Burgess-Brown, F. Von Delft, U. Oppermann, Z. Walters, J. Shipley, F. I. Raynaud, S. M. Westaway, R. K. Prinjha, O. Fedorov, R. Burke, C. J. Schofield, I. M. Westwood, C. Bountra, S. Muller, R. L. M. Van Montfort, P. E. Brennan, J. Blagg
8-Substituted Pyrido[3, 4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, Kdm4 (Jmjd2) And Kdm5 (Jarid1) Histone Lysine Demethylase Inhibitors.
J. Med. Chem. V. 59 1388 2016
PubMed-ID: 26741168  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01635

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: JMJC DOMAIN, RESIDUES 25-101,374-772
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MN2Ligand/IonMANGANESE (II) ION
4QAY1Ligand/Ion2-[(4-{2-ACETYLAMINO-2-[4-(1-CARBOXY-3-METHYLSULFANYL-PROPYLCARBAMOYL)-BUTYLCARBAMOYL]-ETHYL}-2-ETHYL-PHENYL)-OXALYL-AMINO]-BENZOIC ACID
5ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A 800
2AC2SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2058BINDING SITE FOR RESIDUE MN A 801
3AC3SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , QAY A:901 , HOH A:2141BINDING SITE FOR RESIDUE MN A 802
4AC4SOFTWARETYR A:425 , ASP A:428 , TYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , LYS A:517 , TRP A:519 , HIS A:587 , MN A:802 , HOH A:2141BINDING SITE FOR RESIDUE QAY A 901
5AC5SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2206BINDING SITE FOR RESIDUE EDO A1755
6AC6SOFTWAREGLY A:524 , HOH A:2155 , HOH A:2279BINDING SITE FOR RESIDUE EDO A1756
7AC7SOFTWAREILE A:500 , TRP A:504 , ARG A:584 , HIS A:617 , TYR A:618 , LEU A:621BINDING SITE FOR RESIDUE DMS A1757

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:706 -A:723
2A:708 -A:725

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FPL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FPL)

(-) 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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee......eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhh...........hhhhhhh........hhhhh...hhhhh...hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh........ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...........eeeee...........hhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fpl A   0 MFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPKLFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAES 754
                            ||      34        44        54        64        74        84        94     ||377       387       397       407       417       427       437     ||448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748      
                            ||                                                                       100|                                                                  443|                                                                                                                                                                                                                                                                                                                     
                            0|                                                                        374                                                                   445                                                                                                                                                                                                                                                                                                                     
                            26
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  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 5FPL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5fpl
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  KDM5B_HUMAN | Q9UGL1
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM5B_HUMAN | Q9UGL1: 2ma5 2mny 2mnz 5a1f 5a3n 5a3p 5a3t 5a3w 5fpu 5fun 5fup 5fv3 5fy4 5fy5 5fy9 5fyb 5fys 5fyt 5fyu 5fyv 5fyy 5fyz 5fz0 5fz1 5fz3 5fz4 5fz6 5fz7 5fz8 5fz9 5fza 5fzb 5fzc 5fzd 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

(-) Related Entries Specified in the PDB File

5fpu CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH GSKJ1
5fpv CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND KDOAM20A