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(-) Description

Title :  STRUCTURE OF HUMAN G9A SET-DOMAIN (EHMT2) IN COMPLEX WITH INHIBITOR MS0124
 
Authors :  N. Babault, Y. Xiong, J. Liu, J. Jin
Date :  07 Nov 16  (Deposition) - 22 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyl-Transferase Inhibitor Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xiong, F. Li, N. Babault, A. Dong, H. Zeng, H. Wu, X. Chen, C. H. Arrowsmith, P. J. Brown, J. Liu, M. Vedadi, J. Jin
Discovery Of Potent And Selective Inhibitors For G9A-Like Protein (Glp) Lysine Methyltransferase.
J. Med. Chem. V. 60 1876 2017
PubMed-ID: 28135087  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01645

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE EHMT2
    Chains: A, B
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC
    Expression System Strain: BL21 (DE3) CODON PLUS RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 887-1154
    Gene: EHMT2, BAT8, C6ORF30, G9A, KMT1C, NG36
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 2,HLA-B- ASSOCIATED TRANSCRIPT 8,HISTONE H3-K9 METHYLTRANSFERASE 3,H3-K9- HMTASE 3,LYSINE N-METHYLTRANSFERASE 1C,PROTEIN G9A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
17L62Ligand/Ion6,7-DIMETHOXY-N-(1-METHYLPIPERIDIN-4-YL)-2-(MORPHOLIN-4-YL)QUINAZOLIN-4-AMINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
3ZN8Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:980 , CYS A:1017 , CYS A:1023 , CYS A:1027 , ZN A:1503binding site for residue ZN A 1501
02AC2SOFTWARECYS A:974 , CYS A:987 , CYS A:1017 , CYS A:1021binding site for residue ZN A 1502
03AC3SOFTWARECYS A:974 , CYS A:976 , CYS A:980 , CYS A:985 , ZN A:1501binding site for residue ZN A 1503
04AC4SOFTWARECYS A:1115 , CYS A:1168 , CYS A:1170 , CYS A:1175binding site for residue ZN A 1504
05AC5SOFTWAREMET A:1048 , TRP A:1050 , SER A:1084 , TYR A:1085 , ARG A:1109 , ASN A:1112 , HIS A:1113 , TYR A:1154 , PHE A:1166 , GLN A:1169binding site for residue SAM A 1505
06AC6SOFTWAREASP A:1074 , ALA A:1077 , ASP A:1078 , ARG A:1080 , ASP A:1083 , LEU A:1086 , ASP A:1088 , CYS A:1098 , ARG A:1157 , PHE A:1158binding site for residue 7L6 A 1506
07AC7SOFTWARECYS B:980 , CYS B:1017 , CYS B:1023 , CYS B:1027binding site for residue ZN B 1501
08AC8SOFTWARECYS B:974 , CYS B:987 , CYS B:1017 , CYS B:1021binding site for residue ZN B 1502
09AC9SOFTWARECYS B:974 , CYS B:976 , CYS B:980 , CYS B:985binding site for residue ZN B 1503
10AD1SOFTWARECYS B:1115 , CYS B:1168 , CYS B:1170 , CYS B:1175binding site for residue ZN B 1504
11AD2SOFTWAREMET B:1048 , GLY B:1049 , TRP B:1050 , SER B:1084 , TYR B:1085 , ARG B:1109 , PHE B:1110 , ASN B:1112 , HIS B:1113 , TYR B:1154 , PHE B:1166 , CYS B:1168 , GLN B:1169 , HOH B:1630binding site for residue SAM B 1505
12AD3SOFTWAREASP B:1074 , ALA B:1077 , ASP B:1078 , ARG B:1080 , ASP B:1083 , LEU B:1086 , ASP B:1088 , CYS B:1098 , PHE B:1158 , ILE B:1161binding site for residue 7L6 B 1506

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:937 -A:946
2B:937 -B:946

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TUY)

(-) 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:267
                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee............ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhhhh.....eeee.......eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tuy A  921 IICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQS 1187
                                   930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180       


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee............ee..............hhhhh.............hhhhhh.......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhhh......eeee....eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tuy B  923 CRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSK 1188
                                   932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185   
                                                                                                                                                                                                1090|                                                                                              
                                                                                                                                                                                                 1094
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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 5TUY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  EHMT2_HUMAN | Q96KQ7
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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
        EHMT2_HUMAN | Q96KQ7: 2o8j 3dm1 3k5k 3rjw 4nvq 5jhn 5jin 5jiy 5jj0 5t0k 5t0m 5ttf 5vsc

(-) Related Entries Specified in the PDB File

5tuz GLP SET-DOMAIN (EHMT1) IN COMPLEX WITH INHIBITOR MS0124