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(-) Description

Title :  SMYD2 IN COMPLEX WITH AZ931
 
Authors :  A. Ferguson
Date :  20 Jun 16  (Deposition) - 07 Dec 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Tranferase, Histone Methyltransferase, Inhibitor, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Cowen, D. Russell, L. A. Dakin, H. Chen, N. A. Larsen, R. Godin, S. Throner, X. Zheng, A. Molina, J. Wu, T. Cheung, T. Howard, R. Garcia-Arenas, N. Keen, C. S. Pendleton, J. A. Pietenpol, A. D. Ferguson
Design, Synthesis, And Biological Activity Of Substrate Competitive Smyd2 Inhibitors.
J. Med. Chem. V. 59 11079 2016
PubMed-ID: 28002961

(-) Compounds

Molecule 1 - N-LYSINE METHYLTRANSFERASE SMYD2
    Chains: A
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SMYD2, KMT3C
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSKM-B,HISTONE METHYLTRANSFERASE SMYD2,LYSINE N- METHYLTRANSFERASE 3C,SET AND MYND DOMAIN-CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
16TM1Ligand/Ion6-[2-[4-[2-(3,4-DICHLOROPHENYL)ETHYL]PIPERAZIN-1-YL]PHENYL]-~{N}-(3-PYRROLIDIN-1-YLPROPYL)-2~{H}-PYRAZOLO[3,4-B]PYRIDINE-4-CARBOXAMIDE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , LYS A:17 , ARG A:19 , GLU A:135 , HIS A:137 , LYS A:162 , CYS A:181 , ASN A:182 , ALA A:203 , LEU A:204 , ASN A:206 , HIS A:207 , TYR A:240 , TYR A:258 , PHE A:260 , 6TM A:502 , HOH A:616 , HOH A:654 , HOH A:659 , HOH A:709binding site for residue SAM A 501
2AC2SOFTWARETHR A:105 , ILE A:149 , VAL A:179 , ASN A:180 , CYS A:181 , ASN A:182 , GLY A:183 , PHE A:184 , THR A:185 , TYR A:240 , TYR A:258 , SAM A:501 , HOH A:617 , HOH A:715 , HOH A:737 , HOH A:751binding site for residue 6TM A 502
3AC3SOFTWARECYS A:52 , CYS A:55 , CYS A:74 , CYS A:78binding site for residue ZN A 503
4AC4SOFTWARECYS A:65 , CYS A:68 , HIS A:86 , CYS A:90binding site for residue ZN A 504
5AC5SOFTWARECYS A:209 , CYS A:262 , CYS A:264 , CYS A:267binding site for residue ZN A 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KJM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KJM)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....eeeee........eeeeee..eeee.hhhh..............ee.......ee.hhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kjm A   5 GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH 433
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
   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 5KJM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  5kjm
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  SMYD2_HUMAN | Q9NRG4
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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
        SMYD2_HUMAN | Q9NRG4: 3rib 3s7b 3s7d 3s7f 3s7j 3tg4 3tg5 4o6f 4wuy 4ynd 5arf 5arg 5kjk 5kjl 5kjn

(-) Related Entries Specified in the PDB File

5kjk 5kjl 5kjn