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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD7 [N-(3-(((R)-1-(7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDIN-3-YL)(METHYL)AMINO) PROPYL)-2-(3-(2-CHLORO-3-(2-METHYLPYRIDIN-3-YL)BENZO[B]THIOPHEN-5-YL)UREIDO)ACETAMIDE]
 
Authors :  C. Be, E. Koch, C. Gaul, F. Stauffer, H. Moebitz, C. Scheufler
Date :  18 Jan 17  (Deposition) - 22 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
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 :  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 Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
15JU2Ligand/IonN~2~-{[2-CHLORO-3-(2-METHYLPYRIDIN-3-YL)-1-BENZOTHIOPHEN-5-YL]CARBAMOYL}-N-(3-{METHYL[(3R)-1-(5H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDIN-3-YL]AMINO}PROPYL)GLYCINAMIDE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
15JU1Ligand/IonN~2~-{[2-CHLORO-3-(2-METHYLPYRIDIN-3-YL)-1-BENZOTHIOPHEN-5-YL]CARBAMOYL}-N-(3-{METHYL[(3R)-1-(5H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDIN-3-YL]AMINO}PROPYL)GLYCINAMIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
15JU1Ligand/IonN~2~-{[2-CHLORO-3-(2-METHYLPYRIDIN-3-YL)-1-BENZOTHIOPHEN-5-YL]CARBAMOYL}-N-(3-{METHYL[(3R)-1-(5H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDIN-3-YL]AMINO}PROPYL)GLYCINAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:140 , LEU A:143 , VAL A:144 , ASP A:161 , GLY A:163 , SER A:164 , GLY A:165 , VAL A:169 , GLU A:186 , LYS A:187 , GLY A:221 , ASP A:222 , PHE A:223 , PHE A:239 , VAL A:240 , ASN A:241 , VAL A:267 , SER A:268 , SER A:269 , SER A:311 , HOH A:511binding site for residue 5JU A 401
2AC2SOFTWAREASN A:79 , ARG A:80binding site for residue SO4 A 402
3AC3SOFTWARETHR A:100 , ARG A:101 , LYS A:212binding site for residue SO4 A 403
4AC4SOFTWARESER B:140 , LEU B:143 , VAL B:144 , ASP B:161 , GLY B:163 , SER B:164 , GLY B:165 , VAL B:169 , GLU B:186 , LYS B:187 , GLY B:221 , ASP B:222 , PHE B:223 , PHE B:239 , VAL B:240 , ASN B:241 , VAL B:267 , SER B:268 , SER B:269 , SER B:311 , HOH B:506binding site for residue 5JU B 401
5AC5SOFTWAREARG B:8 , LYS B:10 , ASN B:79 , ARG B:80binding site for residue SO4 B 402
6AC6SOFTWARETHR B:100 , ARG B:101 , LYS B:212binding site for residue SO4 B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MW4)

(-) 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 5MW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MW4)

(-) Exons   (0, 0)

(no "Exon" information available for 5MW4)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee............eeeeee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mw4 A   5 LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGNTRPSTGLLRHILQQVYNHSVTDPEKGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKSWTGKPVSYYLHTIDRTILENYFSSLKN 331
                                    14        24        34        44        54        64        74        84      |101       111       121  ||   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      |306       316       326     
                                                                                                                 91|                      124|                                                                                                                                                                300|                           
                                                                                                                  99                       137                                                                                                                                                                 304                           


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......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
                 5mw4 B   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHILQQVYNHSVTDPEKLGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKN 331
                                    13        23        33        43        53        63        73        83        99       109       119     ||140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 
                                                                                                                   92|                       125|                                                                                                                                                                                                  
                                                                                                                    99                        137
   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 5MW4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MW4)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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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 5mvs 5mw3

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