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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH ADENOSINE AND INHIBITOR CPD1 [N6-(2,6-DICHLOROPHENYL)-N6-(PENT-2-YN-1-YL)QUINOLINE-4,6-DIAMINE]
 
Authors :  C. Be, E. Koch, C. Gaul, F. Stauffer, H. Moebitz, C. Scheufler
Date :  17 Jan 17  (Deposition) - 22 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Complex, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mobitz, R. Machauer, P. Holzer, A. Vaupel, F. Stauffer, C. Ragot, G. Caravatti, C. Scheufler, C. Fernandez, U. Hommel, R. Tiedt, K. S. Beyer, C. Chen, H. Zhu, C. Gaul
Discovery Of Potent, Selective, And Structurally Novel Dot1 Inhibitors By A Fragment Linking Approach.
Acs Med Chem Lett V. 8 338 2017
PubMed-ID: 28337327  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00519

(-) 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
    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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
15JJ2Ligand/IonN~6~-(2,6-DICHLOROPHENYL)-N~6~-(PENT-2-YN-1-YL)QUINOLINE-4,6-DIAMINE
2ADN2Ligand/IonADENOSINE
3TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:163 , GLU A:186 , LYS A:187 , ALA A:188 , GLY A:221 , ASP A:222 , PHE A:223 , ASN A:241 , HOH A:553 , HOH A:619binding site for residue ADN A 401
2AC2SOFTWAREPHE A:131 , SER A:140 , LEU A:143 , VAL A:144 , PHE A:239 , VAL A:240 , ASN A:241 , VAL A:267 , SER A:268 , SER A:269 , VAL A:310 , SER A:311 , HOH A:510 , HOH A:618binding site for residue 5JJ A 402
3AC3SOFTWAREGLY A:246 , PRO A:247 , GLU A:248 , VAL A:249 , LYS A:330 , HOH A:570binding site for residue TLA A 403
4AC4SOFTWAREGLY B:163 , GLU B:186 , LYS B:187 , GLY B:221 , ASP B:222 , PHE B:223 , ASN B:241 , PHE B:245 , HOH B:593binding site for residue ADN B 401
5AC5SOFTWAREPHE B:131 , SER B:140 , LEU B:143 , VAL B:144 , PHE B:239 , VAL B:240 , ASN B:241 , VAL B:267 , SER B:268 , SER B:269 , VAL B:310 , SER B:311 , HOH B:575binding site for residue 5JJ B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 5MVS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MVS)

(-) 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 5mvs A   5 LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSWTGKPVSYYLHTIDRTILENYFSSLKNP 332
                                    14        24        34        44        54        64        74        84       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300||     312       322       332
                                                                                                                  92|                                                                                                                                                                                                       301|                            
                                                                                                                   99                                                                                                                                                                                                        304                            


Chain B from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               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.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvs B   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKN 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       309       319       329  
                                                                                                                   92|                                                                                                                                                                                                                                        
                                                                                                                    99
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5MVS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  5mvs
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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 5drt 5dry 5dsx 5dt2 5dtm 5dtq 5dtr 5juw 5mw3 5mw4

(-) Related Entries Specified in the PDB File

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