5F32 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 40

Authors :   Y. -V. Le Bihan, S. Dempster, 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 :   2.05

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 :   Oxidoreductase, Epigenetics, Demethylase, Inhibitor (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
	Expression System Plasmid	:	PNIC28
	Expression System Taxid	:	562
	Expression System Variant	:	ROSETTA (DE3)
	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 (5, 26)

No.	Name	Count	Type	Full Name
1	5V7	4	Ligand/Ion	8-(2-AZANYL-1,3-THIAZOL-4-YL)-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	DMS	6	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	4	Ligand/Ion	GLYCEROL
5	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	5V7	1	Ligand/Ion	8-(2-AZANYL-1,3-THIAZOL-4-YL)-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	5V7	1	Ligand/Ion	8-(2-AZANYL-1,3-THIAZOL-4-YL)-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	5V7	1	Ligand/Ion	8-(2-AZANYL-1,3-THIAZOL-4-YL)-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	-1	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (4, 7)

No.	Name	Count	Type	Full Name
1	5V7	1	Ligand/Ion	8-(2-AZANYL-1,3-THIAZOL-4-YL)-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	2	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , 5V7 A:403 , HOH A:520	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 , TYR A:177 , PHE A:185 , HIS A:188 , GLU A:190 , LYS A:206 , TRP A:208 , HIS A:276 , ZN A:401 , DMS A:404 , HOH A:520 , HOH A:566	binding site for residue 5V7 A 403
04	AC4	SOFTWARE	GLY A:170 , GLU A:190 , SER A:288 , ASN A:290 , 5V7 A:403	binding site for residue DMS A 404
05	AC5	SOFTWARE	PHE A:27 , ASP A:146 , TRP A:148 , ASN A:149 , ARG A:152 , LEU A:153	binding site for residue EDO A 405
06	AC6	SOFTWARE	VAL A:75 , THR A:76 , GLY A:77 , THR A:126 , PHE A:127 , HOH A:526 , VAL C:75 , THR C:76 , GLY C:77 , THR C:126 , PHE C:127	binding site for residue GOL A 406
07	AC7	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , 5V7 B:403 , HOH B:502	binding site for residue ZN B 401
08	AC8	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	binding site for residue ZN B 402
09	AC9	SOFTWARE	TYR B:132 , TYR B:177 , PHE B:185 , HIS B:188 , GLU B:190 , LYS B:206 , TRP B:208 , HIS B:276 , ZN B:401 , DMS B:404 , HOH B:502 , HOH B:509 , HOH B:580	binding site for residue 5V7 B 403
10	AD1	SOFTWARE	GLY B:170 , TYR B:175 , TYR B:177 , GLU B:190 , SER B:288 , 5V7 B:403	binding site for residue DMS B 404
11	AD2	SOFTWARE	ASN B:102 , CYS B:107 , THR B:108 , GLY B:282 , PHE B:283 , HOH B:579	binding site for residue EDO B 405
12	AD3	SOFTWARE	VAL 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:642	binding site for residue GOL B 406
13	AD4	SOFTWARE	HIS C:188 , GLU C:190 , HIS C:276 , 5V7 C:403 , HOH C:506	binding site for residue ZN C 401
14	AD5	SOFTWARE	CYS C:234 , HIS C:240 , CYS C:306 , CYS C:308	binding site for residue ZN C 402
15	AD6	SOFTWARE	TYR 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 , DMS C:404 , HOH C:506 , HOH C:575	binding site for residue 5V7 C 403
16	AD7	SOFTWARE	GLY C:170 , TYR C:177 , GLU C:190 , SER C:288 , ASN C:290 , 5V7 C:403	binding site for residue DMS C 404
17	AD8	SOFTWARE	THR C:16	binding site for residue DMS C 405
18	AD9	SOFTWARE	HIS D:188 , GLU D:190 , HIS D:276 , 5V7 D:403	binding site for residue ZN D 401
19	AE1	SOFTWARE	CYS D:234 , HIS D:240 , CYS D:306 , CYS D:308	binding site for residue ZN D 402
20	AE2	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 , DMS D:404 , HOH D:595	binding site for residue 5V7 D 403
21	AE3	SOFTWARE	GLY D:170 , TYR D:175 , TYR D:177 , GLU D:190 , SER D:288 , ASN D:290 , 5V7 D:403	binding site for residue DMS D 404
22	AE4	SOFTWARE	TRP D:332	binding site for residue DMS D 405
23	AE5	SOFTWARE	HIS D:201 , PHE D:202 , HOH D:520	binding site for residue EDO D 406
24	AE6	SOFTWARE	PHE D:114 , GLU D:263	binding site for residue EDO D 407
25	AE7	SOFTWARE	GLU D:214 , HIS D:215 , ARG D:218 , HOH D:619	binding site for residue GOL D 408
26	AE8	SOFTWARE	LEU D:248 , LYS D:251 , LYS D:252	binding site for residue GOL D 409

(no "SS Bond" information available for 5F32)

(no "Cis Peptide Bond" information available for 5F32)

(no "SAP(SNP)/Variant" information available for 5F32)

(no "PROSITE Motif" information available for 5F32)

(no "Exon" information available for 5F32)

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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               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.hhhhhhhhhhh.........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
                 5f32 A  11 SARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       312       322       332       342       352  
                                                                                                                                                                                                                                                                                                                                    309|                                          
                                                                                                                                                                                                                                                                                                                                     312

Chain B from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               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.hhhhhhhhhh..........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
                 5f32 B  11 SARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain C from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhh...........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f32 C   6 ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK 355
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355

Chain D from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhh...........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
                 5f32 D   6 ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5F32)

(no "CATH Domain" information available for 5F32)

(no "Pfam Domain" information available for 5F32)

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Description

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Ligands, Modified Residues, Ions (5, 26)

Sites (26, 26)

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