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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD1 [4-(2,6-DICHLOROBENZOYL)-N-METHYL-1H-PYRROLE-2-CARBOXAMIDE]
 
Authors :  C. Scheufler, C. Be, H. Moebitz, F. Stauffer
Date :  18 Sep 15  (Deposition) - 15 Jun 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Complex, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Scheufler, H. Mobitz, C. Gaul, C. Ragot, C. Be, C. Fernandez, K. S. Beyer, R. Tiedt, F. Stauffer
Optimization Of A Fragment-Based Screening Hit Toward Poten Dot1L Inhibitors Interacting In An Induced Binding Pocket.
Acs Med. Chem. Lett. V. 7 730 2016
PubMed-ID: 27563394  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00168

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC
    ChainsA, B
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDOT1L, KIAA1814, KMT4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOT1-LIKE PROTEIN,HISTONE H3-K79 METHYLTRANSFERASE,H3-K79- HMTASE,LYSINE N-METHYLTRANSFERASE 4

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15F42Ligand/Ion4-(2,6-DICHLOROBENZOYL)-N-METHYL-1H-PYRROLE-2-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15F41Ligand/Ion4-(2,6-DICHLOROBENZOYL)-N-METHYL-1H-PYRROLE-2-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15F41Ligand/Ion4-(2,6-DICHLOROBENZOYL)-N-METHYL-1H-PYRROLE-2-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:131 , SER A:140 , LEU A:143 , VAL A:144 , PHE A:239 , ASN A:241 , PHE A:243 , VAL A:267 , SER A:268 , SER A:269 , SER A:311 , TYR A:312 , HOH A:550 , HOH A:552 , HOH A:562 , HOH A:635binding site for residue 5F4 A 401
2AC2SOFTWAREPHE B:131 , SER B:140 , LEU B:143 , VAL B:144 , PHE B:239 , ASN B:241 , PHE B:243 , VAL B:267 , SER B:268 , SER B:269 , SER B:311 , TYR B:312 , HOH B:579 , HOH B:607binding site for residue 5F4 B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:22 -Pro A:23
2Trp B:22 -Pro B:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DTM)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhh.....hhhhh..hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee.............eeeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dtm A   5 LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSWTGKPVSYYLHTIDRTILENYFSSLKNP 332
                                    14        24        34        44        54        64        74        84      |101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301|      313       323         
                                                                                                                 91|                                                                                                                                                                                                       301|                            
                                                                                                                  99                                                                                                                                                                                                        304                            

Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhh.....hhhhh..hhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee............eeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dtm B   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKSWTGKPVSYYLHTIDRTILENYFSSLKN 331
                                    13        23        33        43        53        63        73        83        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299||     312       322         
                                                                                                                   92|                                                                                                                                                                                                      300|                           
                                                                                                                    99                                                                                                                                                                                                       304                           

   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 5DTM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DOT1L_HUMAN | Q8TEK31nw3 2mv7 3qow 3qox 3sr4 3sx0 3uwp 4ek9 4ekg 4eki 4eqz 4er0 4er3 4er5 4er6 4er7 4hra 4wvl 5drt 5dry 5dsx 5dt2 5dtq 5dtr 5juw 5mvs 5mw3 5mw4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DTM)