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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD2 [2-(2-(5-((2-CHLOROPHENOXY)METHYL)-1H-TETRAZOL-1-YL)ACETYL)-N-(4-CHLOROPHENYL)HYDRAZINECARBOXAMIDE]
 
Authors :  C. Scheufler, C. Gaul, C. Be, H. Moebitz
Date :  16 Sep 15  (Deposition) - 15 Jun 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
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. Chen, H. Zhu, F. Stauffer, G. Caravatti, S. Vollmer, R. Machauer, P. Holzer, H. Mobitz, C. Scheufler, M. Klumpp, R. Tiedt, K. S. Beyer, K. Calkins, D. Guthy, M. Kiffe, J. Zhang, C. Gaul
Discovery Of Novel Dot1L Inhibitors Through A Structure-Based Fragmentation Approach.
Acs Med. Chem. Lett. V. 7 735 2016
PubMed-ID: 27563395  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00167

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC
    Chains: A, B
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-333
    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

  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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
15EG2Ligand/Ion2-({5-[(2-CHLOROPHENOXY)METHYL]-1H-TETRAZOL-1-YL}ACETYL)-N-(4-CHLOROPHENYL)HYDRAZINECARBOXAMIDE
2K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15EG1Ligand/Ion2-({5-[(2-CHLOROPHENOXY)METHYL]-1H-TETRAZOL-1-YL}ACETYL)-N-(4-CHLOROPHENYL)HYDRAZINECARBOXAMIDE
2K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15EG1Ligand/Ion2-({5-[(2-CHLOROPHENOXY)METHYL]-1H-TETRAZOL-1-YL}ACETYL)-N-(4-CHLOROPHENYL)HYDRAZINECARBOXAMIDE
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:131 , PRO A:133 , SER A:140 , ASP A:161 , GLY A:163 , SER A:164 , GLY A:165 , VAL A:166 , GLN A:168 , VAL A:169 , VAL A:240 , ASN A:241 , VAL A:267 , SER A:268 , SER A:269binding site for residue 5EG A 401
2AC2SOFTWARELYS B:52 , LEU B:53 , MET B:55 , ASN B:57binding site for residue K B 1001
3AC3SOFTWAREPHE B:131 , PRO B:133 , TYR B:136 , SER B:140 , ASP B:161 , GLY B:163 , SER B:164 , GLY B:165 , VAL B:166 , GLN B:168 , VAL B:169 , PHE B:239 , VAL B:240 , ASN B:241 , VAL B:267 , SER B:268 , SER B:269binding site for residue 5EG B 1002

(-) SS Bonds  (0, 0)

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

(-) 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 5DRT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DRT)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee.............eeeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5drt A   5 LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGNTRPSTGLLRHILQQVYNHSVTDPEKLFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSWTGKPVSYYLHTIDRTILENYFSSLKNP 332
                                    14        24        34        44        54        64        74        84      |101       111       121   ||  136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    || 308       318       328    
                                                                                                                 91|                       125|                                                                                                                                                                       301|                            
                                                                                                                  99                        131                                                                                                                                                                        304                            


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhh.hhhhh..hhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee............eeeeee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5drt B   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHILQQVYNHSVTDPEKLFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKSWTGKPVSYYLHTIDRTILENYFSSLKN 331
                                    13        23        33        43        53        63        73        83        99       109       119     ||134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     ||307       317       327    
                                                                                                                   92|                       125|                                                                                                                                                                      300|                           
                                                                                                                    99                        131                                                                                                                                                                       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 5DRT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  5drt
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  DOT1L_HUMAN | Q8TEK3
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  2.1.1.43
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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 4hra 4wvl 5dry 5dsx 5dt2 5dtm 5dtq 5dtr 5juw 5mvs 5mw3 5mw4

(-) Related Entries Specified in the PDB File

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