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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 54A
 
Authors :  Y. -V. Le Bihan, I. M. Westwood, R. L. M. Van Montfort
Date :  02 Dec 15  (Deposition) - 20 Jan 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Epigenetics, Demethylase, Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Bavetsias, R. M. Lanigan, G. F. Ruda, B. Atrash, M. G. Mclaughlin, A. Tumber, N. Y. Mok, Y. V. Le Bihan, S. Dempster, K. J. Boxall, F. Jeganathan, S. B. Hatch, P. Savitsky, S. Velupillai, T. Krojer, K. S. England, J. Sejberg, C. Thai, A. Donovan, A. Pal, G. Scozzafava, J. M. Bennett, A. Kawamura, C. Johansson, A. Szykowska, C. Gileadi, N. A. Burgess-Brown, F. Von Delft, U. Oppermann, Z. Walters, J. Shipley, F. I. Raynaud, S. M. Westaway, R. K. Prinjha, O. Fedorov, R. Burke, C. J. Schofield, I. M. Westwood, C. Bountra, S. Muller, R. L. Van Montfort, P. E. Brennan, J. Blagg
8-Substituted Pyrido[3, 4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, Kdm4 (Jmjd2) And Kdm5 (Jarid1) Histone Lysine Demethylase Inhibitors.
J. Med. Chem. V. 59 1388 2016
PubMed-ID: 26741168  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01635

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
    Chains: A, B, C, D
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PLASMID
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JUMONJI DOMAIN-CONTAINING PROTEIN 2A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
15UO4Ligand/Ion8-[4-[2-[4-(4-CHLOROPHENYL)PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3GOL2Ligand/IonGLYCEROL
4ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
15UO1Ligand/Ion8-[4-[2-[4-(4-CHLOROPHENYL)PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3GOL-1Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
15UO1Ligand/Ion8-[4-[2-[4-(4-CHLOROPHENYL)PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
15UO1Ligand/Ion8-[4-[2-[4-(4-CHLOROPHENYL)PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
15UO1Ligand/Ion8-[4-[2-[4-(4-CHLOROPHENYL)PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3GOL-1Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:188 , GLU A:190 , HIS A:276 , 5UO A:403 , HOH A:514binding site for residue ZN A 401
02AC2SOFTWARECYS A:234 , HIS A:240 , CYS A:306 , CYS A:308binding site for residue ZN A 402
03AC3SOFTWARETYR A:132 , ASP A:135 , TYR A:177 , PHE A:185 , HIS A:188 , GLU A:190 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , ZN A:401 , HOH A:514binding site for residue 5UO A 403
04AC4SOFTWARETYR A:59 , ARG A:98binding site for residue DMS A 404
05AC5SOFTWAREHIS B:188 , GLU B:190 , HIS B:276 , 5UO B:403binding site for residue ZN B 401
06AC6SOFTWARECYS B:234 , HIS B:240 , CYS B:306 , CYS B:308binding site for residue ZN B 402
07AC7SOFTWARETYR B:132 , ASP B:135 , TYR B:175 , TYR B:177 , PHE B:185 , HIS B:188 , GLU B:190 , LYS B:206 , TRP B:208 , HIS B:276 , ZN B:401binding site for residue 5UO B 403
08AC8SOFTWAREVAL B:75 , THR B:76 , GLY B:77 , THR B:126 , PHE B:127 , VAL D:75 , THR D:76 , GLY D:77 , THR D:126 , PHE D:127 , HOH D:522binding site for residue GOL B 404
09AC9SOFTWAREHIS C:188 , GLU C:190 , HIS C:276 , 5UO C:403 , HOH C:502binding site for residue ZN C 401
10AD1SOFTWARECYS C:234 , HIS C:240 , CYS C:306 , CYS C:308binding site for residue ZN C 402
11AD2SOFTWARETYR C:132 , TYR C:177 , PHE C:185 , HIS C:188 , GLU C:190 , LYS C:206 , TRP C:208 , LYS C:241 , HIS C:276 , ZN C:401 , HOH C:502binding site for residue 5UO C 403
12AD3SOFTWAREVAL A:75 , THR A:76 , GLY A:77 , THR A:126 , PHE A:127 , HOH A:566 , VAL C:75 , THR C:76 , GLY C:77 , THR C:126 , PHE C:127binding site for residue GOL C 404
13AD4SOFTWAREARG C:294 , PHE C:324binding site for residue DMS C 405
14AD5SOFTWAREHIS D:188 , GLU D:190 , HIS D:276 , 5UO D:403 , HOH D:507binding site for residue ZN D 401
15AD6SOFTWARECYS D:234 , HIS D:240 , CYS D:306 , CYS D:308binding site for residue ZN D 402
16AD7SOFTWARETYR D:132 , ASP D:135 , TYR D:177 , PHE D:185 , HIS D:188 , GLU D:190 , LYS D:206 , TRP D:208 , HIS D:276 , ZN D:401 , HOH D:507binding site for residue 5UO D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F3E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F3E)

(-) Exons   (0, 0)

(no "Exon" information available for 5F3E)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee...........hhhhh.hhhhhh....eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh...........hhhhhhhhhhhhhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3e A   6 ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155    || 175       185       195       205       215       225       235       245       255       265       275       285       295       305   ||  317       327       337       347       
                                                                                                                                                                                    160|                                                                                                                                       309|                                          
                                                                                                                                                                                     171                                                                                                                                        312                                          


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee...........hhhhh.hhhhhh....eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh...........hhhhhhhhh..hhhhhhh............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3e B   7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156   ||  176       186       196       206       216       226       236       246       256       266       276       286       296       306  ||   318       328       338       348     
                                                                                                                                                                                   160|                                                                                                                                       309|                                         
                                                                                                                                                                                    171                                                                                                                                        312                                         


Chain C from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee...........hhhhh.hhhhhhhhhhh.......eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh..........hhhhhhhhh..hhhhhhhh...........hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3e C  10 PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       171       181       191       201       211       221       231       241       251       261       271       281       291       301      |314       324       334       344       354
                                                                                                                                                                                        168|                                                                                                                                      308|                                          
                                                                                                                                                                                         171                                                                                                                                       312                                          


Chain D from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee...........hhhhh.hhhhhhh.....eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh...........hhhhhhhhh..hhhhhhh............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3e D  10 PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 ||    177       187       197       207       217       227       237       247       257       267       277       287       297       307 ||    319       329       339       349     
                                                                                                                                                                                 161|                                                                                                                                        309|                                          
                                                                                                                                                                                  170                                                                                                                                         312
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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 5F3E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F3E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F3E)

(-) Gene Ontology  (25, 25)

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  5f3e
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  KDM4A_HUMAN | O75164
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KDM4A_HUMAN | O75164: 2gf7 2gfa 2gp3 2gp5 2oq6 2oq7 2os2 2ot7 2ox0 2p5b 2pxj 2q8c 2q8d 2q8e 2qqr 2qqs 2vd7 2wwj 2ybk 2ybp 2ybs 3njy 3pdq 3rvh 3u4s 4ai9 4bis 4gd4 4ura 4v2v 4v2w 5a7n 5a7o 5a7p 5a7q 5a7s 5a7w 5a80 5anq 5d6w 5d6x 5d6y 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3g 5f3i 5f5i 5fpv 5fwe 5fy8 5fyc 5fyh 5fyi 5ly1 5ly2 5tvr 5tvs

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