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(-) Description

Title :  CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD3 [N-(1-(2-CHLOROPHENYL)-1H-INDOL-6-YL)-2-(2-(5-(2-CHLOROPHENYL)-1H-TETRAZOL-1-YL)ACETYL)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 :  2.41
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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
15EK2Ligand/IonN-[1-(2-CHLOROPHENYL)-1H-INDOL-6-YL]-2-{[5-(2-CHLOROPHENYL)-1H-TETRAZOL-1-YL]ACETYL}HYDRAZINECARBOXAMIDE
2K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15EK1Ligand/IonN-[1-(2-CHLOROPHENYL)-1H-INDOL-6-YL]-2-{[5-(2-CHLOROPHENYL)-1H-TETRAZOL-1-YL]ACETYL}HYDRAZINECARBOXAMIDE
2K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15EK1Ligand/IonN-[1-(2-CHLOROPHENYL)-1H-INDOL-6-YL]-2-{[5-(2-CHLOROPHENYL)-1H-TETRAZOL-1-YL]ACETYL}HYDRAZINECARBOXAMIDE
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:53 , MET A:55 , ASN A:57 , HOH A:591 , HOH A:614binding site for residue K A 401
2AC2SOFTWAREPHE A:131 , PRO A:133 , TYR A:136 , SER A:140 , LEU A:143 , VAL A:144 , MET A:147 , ASP A:161 , GLY A:163 , SER A:164 , GLY A:165 , VAL A:166 , GLN A:168 , VAL A:240 , ASN A:241 , VAL A:267 , SER A:268 , HOH A:516binding site for residue 5EK A 402
3AC3SOFTWARELYS B:52 , LEU B:53 , MET B:55 , ASN B:57binding site for residue K B 1001
4AC4SOFTWAREPHE B:131 , PRO B:133 , TYR B:136 , SER B:140 , LEU B:143 , VAL B:144 , MET B:147 , ASP B:161 , GLY B:163 , SER B:164 , GLY B:165 , VAL B:166 , GLN B:168 , PHE B:239 , VAL B:240 , ASN B:241 , VAL B:267 , SER B:268 , SER B:269 , HOH B:1143binding site for residue 5EK B 1002

(-) SS Bonds  (0, 0)

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

(-) 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 5DRY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DRY)

(-) 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..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee............eeeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dry A   5 LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKSWTGKPVSYYLHTIDRTILENYFSSLKNP 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|      313       323         
                                                                                                                  92|                                                                                                                                                                                                      300|                            
                                                                                                                   99                                                                                                                                                                                                       304                            


Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee.............eeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dry B   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKVSWTGKPVSYYLHTIDRTILENYFSSLKN 331
                                    13        23        33        43        53        63        73        83        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 ||    310       320       330 
                                                                                                                   92|                                                                                                                                                                                                       300|                            
                                                                                                                    98                                                                                                                                                                                                        303
   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 5DRY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

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