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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH EPZ-5676
 
Authors :  L. Jin
Date :  26 Oct 12  (Deposition) - 31 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone Lysine Methyltransferase, Transferase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Daigle, E. J. Olhava, C. A. Therkelsen, A. Basavapathruni, L. Jin P. A. Boriack-Sjodin, C. J. Allain, C. R. Klaus, A. Raimondi, M. P. Scott, N. J. Waters, R. Chesworth, M. P. Moyer, R. A. Copeland, V. M. Richon, R. M. Pollock
Potent Inhibition Of Dot1L As Treatment Of Mll-Fusion Leukemia.
Blood V. 122 1017 2013
PubMed-ID: 23801631  |  Reference-DOI: 10.1182/BLOOD-2013-04-497644

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-416
    Gene: DOT1L, KIAA1814, KMT4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOT1-LIKE PROTEIN, HISTONE H3-K79 METHYLTRANSFERASE, H3-K79- HMTASE, LYSINE N-METHYLTRANSFERASE 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EP61Ligand/Ion5'-[{CIS-3-[2-(5-TERT-BUTYL-1H-BENZIMIDAZOL-2-YL)ETHYL]CYCLOBUTYL}(PROPAN-2-YL)AMINO]-5'-DEOXYADENOSINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:161 , GLY A:163 , SER A:164 , GLY A:165 , VAL A:169 , VAL A:185 , GLU A:186 , LYS A:187 , GLY A:221 , ASP A:222 , PHE A:223 , PHE A:239 , ASN A:241BINDING SITE FOR RESIDUE EP6 A 501
2AC2SOFTWAREASN A:99 , ARG A:101 , LYS A:212BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREHIS A:251 , ASP A:286 , ILE A:287BINDING SITE FOR RESIDUE SO4 A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HRA)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HRA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HRA)

(-) Exons   (0, 0)

(no "Exon" information available for 4HRA)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4hraa_ A: automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh......eeee....hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh.....eeee...........hhhhh.hhhh.eeeeee............eeeeee.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hra A   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPTSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVGKPVSYYLHTIDRTILENYFSSLKNPKL 334
                                    13        23        33        43        53        63        73        83        93       103       113       123      |141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 ||    314       324       334
                                                                                                                                                        130|                                                                                                                                                                 303|                           
                                                                                                                                                         139                                                                                                                                                                  307
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HRA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HRA)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  DOT1L_HUMAN | Q8TEK3
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 Related Entries

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

UniProtKB/Swiss-Prot
        DOT1L_HUMAN | Q8TEK3: 1nw3 2mv7 3qow 3qox 3sr4 3sx0 3uwp 4ek9 4ekg 4eki 4eqz 4er0 4er3 4er5 4er6 4er7 4wvl 5drt 5dry 5dsx 5dt2 5dtm 5dtq 5dtr 5juw 5mvs 5mw3 5mw4

(-) Related Entries Specified in the PDB File

3qow CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH SAM
3qox CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH SAH
4ek9 CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH EPZ000004
4ekg CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH EPZ003696
4eki CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH EPZ004777