5F3G - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 53A

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 :   2.50

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

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	:	ROSETTA2
	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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (4, 20)

No.	Name	Count	Type	Full Name
1	5UL	4	Ligand/Ion	8-[4-[2-[4-[(4-CHLOROPHENYL)METHYL]PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	DMS	7	Ligand/Ion	DIMETHYL SULFOXIDE
4	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	5UL	1	Ligand/Ion	8-[4-[2-[4-[(4-CHLOROPHENYL)METHYL]PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	5UL	1	Ligand/Ion	8-[4-[2-[4-[(4-CHLOROPHENYL)METHYL]PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	5UL	1	Ligand/Ion	8-[4-[2-[4-[(4-CHLOROPHENYL)METHYL]PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	5UL	1	Ligand/Ion	8-[4-[2-[4-[(4-CHLOROPHENYL)METHYL]PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , 5UL A:403	binding site for residue ZN A 401
02	AC2	SOFTWARE	CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308	binding site for residue ZN A 402
03	AC3	SOFTWARE	TYR A:132 , ASP A:135 , GLY A:170 , 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	binding site for residue 5UL A 403
04	AC4	SOFTWARE	TRP A:332	binding site for residue DMS A 404
05	AC5	SOFTWARE	THR A:173	binding site for residue DMS A 405
06	AC6	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , 5UL B:403	binding site for residue ZN B 401
07	AC7	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	binding site for residue ZN B 402
08	AC8	SOFTWARE	TYR B:132 , 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:401 , HOH B:537	binding site for residue 5UL B 403
09	AC9	SOFTWARE	HIS C:188 , GLU C:190 , HIS C:276 , 5UL C:403	binding site for residue ZN C 401
10	AD1	SOFTWARE	CYS C:234 , HIS C:240 , CYS C:306 , CYS C:308	binding site for residue ZN C 402
11	AD2	SOFTWARE	TYR C:132 , ASP C:135 , TYR C:175 , TYR C:177 , PHE C:185 , HIS C:188 , GLU C:190 , LYS C:206 , TRP C:208 , HIS C:276 , ZN C:401	binding site for residue 5UL C 403
12	AD3	SOFTWARE	TYR C:59 , PHE C:202	binding site for residue DMS C 405
13	AD4	SOFTWARE	LYS C:89	binding site for residue DMS C 406
14	AD5	SOFTWARE	HIS D:188 , GLU D:190 , HIS D:276 , 5UL D:403	binding site for residue ZN D 401
15	AD6	SOFTWARE	CYS D:234 , HIS D:240 , CYS D:306 , CYS D:308	binding site for residue ZN D 402
16	AD7	SOFTWARE	TYR D:132 , TYR D:177 , PHE D:185 , HIS D:188 , GLU D:190 , LYS D:206 , TRP D:208 , LYS D:241 , HIS D:276 , ZN D:401	binding site for residue 5UL D 403
17	AD8	SOFTWARE	HIS D:240	binding site for residue DMS D 404
18	AD9	SOFTWARE	THR D:83 , PHE D:227 , SER D:230 , THR D:243	binding site for residue DMS D 405

(no "SS Bond" information available for 5F3G)

(no "Cis Peptide Bond" information available for 5F3G)

(no "SAP(SNP)/Variant" information available for 5F3G)

(no "PROSITE Motif" information available for 5F3G)

(no "Exon" information available for 5F3G)

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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee...........hhhhh.hhhhhhhhhh.....eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee...hhhhhhhhh..........hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3g A   8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      |172       182       192       202       212       222       232       242       252       262       272       282       292       302     ||315       325       335       345         
                                                                                                                                                                                      164|                                                                                                                                       308|                                          
                                                                                                                                                                                       170                                                                                                                                        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...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhh......eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh...........hhhhhhhhhhhhhhhhhh............hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3g B   9 NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158  ||   176       186       196       206       216       226       236       246       256       266       276       286       296       306  ||   318       328       338       348     
                                                                                                                                                                                  161|                                                                                                                                        309|                                         
                                                                                                                                                                                   170                                                                                                                                         312

Chain C from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhh......eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh...........hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3g C   8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157   ||  175       185       195       205       215       225       235       245       255       265       275       285       295       305   ||  317       327       337       347       
                                                                                                                                                                                   161|                                                                                                                                        309|                                          
                                                                                                                                                                                    170                                                                                                                                         312

Chain D from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhh........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh..........hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3g D  11 SARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       172       182       192       202       212       222       232       242       252       262       272       282       292       302     ||315       325       335       345         
                                                                                                                                                                                       168|                                                                                                                                      308|                                          
                                                                                                                                                                                        171                                                                                                                                       312

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(no "SCOP Domain" information available for 5F3G)

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Description

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Ligands, Modified Residues, Ions (4, 20)

Sites (18, 18)

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