5FP3 - JenaLib

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Title :   CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KDM5) FAMILIES OF HISTONE LYSINE DEMETHYLASES

Authors :   C. Chung

Date :   27 Nov 15 (Deposition) - 27 Jan 16 (Release) - 09 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxidoreductase, Inhibitor, Jmjd3, Kdm6B, Jumonji (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Westaway, A. G. S. Preston, M. D. Barker, F. Brown, J. A. Brown, M. Campbell, C. Chung, H. Diallo, C. Douault, G. Drewes, R. Eagle, L. Gordon, C. Haslam, T. G. Hayhow, P. G. Humphreys, G. Joberty, R. Katso, L. Kruidenier, M. Leveridge, J. Liddle, J. Mosley, M. Muelbaier, R. Randle, I. Rioja, A. Rueger, G. A. Seal, R. J. Sheppard O. Singh, J. Taylor, P. Thomas, D. Thomson, D. M. Wilson, K. Lee, R. K. Prinjha
Cell Penetrant Inhibitors Of The Kdm4 And Kdm5 Families Of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives.
J. Med. Chem. V. 59 1357 2016
PubMed-ID: 26771107 | Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01537

Molecule 1 - HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	CATALYTIC DOMAIN, UNP RESIDUES 1141-1643
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JMJC DOMAIN-CONTAINING PROTEIN 3, JUMONJI DOMAIN-CONTAINING PROTEIN 3, LYSINE DEMETHYLASE 6B, JMJD3

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 14)

No.	Name	Count	Type	Full Name
1	3JI	2	Ligand/Ion	3-(4-PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLICACID
2	BCN	4	Ligand/Ion	BICINE
3	CO	2	Ligand/Ion	COBALT (II) ION
4	MG	4	Ligand/Ion	MAGNESIUM ION
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	3JI	1	Ligand/Ion	3-(4-PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLICACID
2	BCN	2	Ligand/Ion	BICINE
3	CO	-1	Ligand/Ion	COBALT (II) ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	3JI	1	Ligand/Ion	3-(4-PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLICACID
2	BCN	2	Ligand/Ion	BICINE
3	CO	-1	Ligand/Ion	COBALT (II) ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:1246 , GLN A:1248 , THR A:1330 , TYR A:1379 , LYS A:1381 , ARG A:1386 , THR A:1387 , PRO A:1388 , HIS A:1390 , ASN A:1400 , TRP A:1410 , HIS A:1470 , HOH A:2002 , HOH A:2003 , BCN A:2640 , BCN A:2641 , CO A:3000	BINDING SITE FOR RESIDUE 3JI A 1
02	AC2	SOFTWARE	CYS A:1575 , CYS A:1578 , CYS A:1602 , CYS A:1605	BINDING SITE FOR RESIDUE ZN A2000
03	AC3	SOFTWARE	GLU A:1415 , GLU A:1498 , HOH A:2247 , HOH A:2248 , HOH A:2291 , HOH A:2295 , HOH A:2458 , HOH A:2459	BINDING SITE FOR RESIDUE MG A2639
04	AC4	SOFTWARE	3JI A:1 , ARG A:1246 , LEU A:1433 , GLY A:1435 , HOH A:2222 , HOH A:2268 , BCN A:2641 , MG A:2642	BINDING SITE FOR RESIDUE BCN A2640
05	AC5	SOFTWARE	3JI A:1 , HIS A:1390 , GLN A:1391 , ASN A:1393 , BCN A:2640 , MG A:2642	BINDING SITE FOR RESIDUE BCN A2641
06	AC6	SOFTWARE	BCN A:2640 , BCN A:2641	BINDING SITE FOR RESIDUE MG A2642
07	AC7	SOFTWARE	3JI A:1 , HIS A:1390 , GLU A:1392 , HIS A:1470 , HOH A:2002 , HOH A:2003	BINDING SITE FOR RESIDUE CO A3000
08	AC8	SOFTWARE	ARG B:1246 , GLN B:1248 , SER B:1270 , THR B:1330 , TYR B:1379 , LYS B:1381 , ARG B:1386 , THR B:1387 , PRO B:1388 , HIS B:1390 , ASN B:1400 , TRP B:1410 , HIS B:1470 , HOH B:2001 , HOH B:2002 , BCN B:2640 , BCN B:2641 , CO B:3000	BINDING SITE FOR RESIDUE 3JI B 1
09	AC9	SOFTWARE	CYS B:1575 , CYS B:1578 , CYS B:1602 , CYS B:1605	BINDING SITE FOR RESIDUE ZN B2000
10	BC1	SOFTWARE	GLU B:1415 , GLU B:1498 , HOH B:2187 , HOH B:2188 , HOH B:2232 , HOH B:2345 , HOH B:2346 , HOH B:2347	BINDING SITE FOR RESIDUE MG B2639
11	BC2	SOFTWARE	3JI B:1 , ARG B:1246 , PRO B:1388 , THR B:1434 , HOH B:2172 , BCN B:2641 , MG B:2642	BINDING SITE FOR RESIDUE BCN B2640
12	BC3	SOFTWARE	3JI B:1 , HIS B:1390 , ILE B:1511 , HOH B:2172 , HOH B:2205 , BCN B:2640 , MG B:2642	BINDING SITE FOR RESIDUE BCN B2641
13	BC4	SOFTWARE	BCN B:2640 , BCN B:2641	BINDING SITE FOR RESIDUE MG B2642
14	BC5	SOFTWARE	3JI B:1 , HIS B:1390 , GLU B:1392 , HIS B:1470 , HOH B:2001 , HOH B:2002	BINDING SITE FOR RESIDUE CO B3000

(no "SS Bond" information available for 5FP3)

Asymmetric Unit

No.	Residues
1	Gly A:1404	-	Pro A:1405
2	Gly B:1404	-	Pro B:1405

(no "SAP(SNP)/Variant" information available for 5FP3)

(no "PROSITE Motif" information available for 5FP3)

(no "Exon" information available for 5FP3)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..hhhhhhhhhhhhhhh.....eeeeehhhhhh..hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhhhhh......hhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........ee......ee..eeeeee.......eeeehhhhhhhh.......eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fp3 A 1177 PREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286     |1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593      1603      1613      1623      1633     
                                                                                                                                            1292|                                                                                                                                                                                                                                                                                                                              
                                                                                                                                             1320

Chain B from PDB  Type:PROTEIN  Length:423
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhh....eeeeehhhhhh..hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhh...eeeeeeeee......hhhhhhhhhhhhhhhh......hhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....................eeeee...eeehhhhhhhh.......eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fp3 B 1180 KLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289  ||  1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589||    1605      1615      1625      1635   
                                                                                                                                         1292|                                                                                                                                                                                                                                                                       1590|                                         
                                                                                                                                          1323                                                                                                                                                                                                                                                                        1597

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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 5FP3)

(no "CATH Domain" information available for 5FP3)

(no "Pfam Domain" information available for 5FP3)

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5fp4	CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-( 4-PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLIC ACID
5fp7	CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 -METHYLTHIOPHEN-2-YL METHYLAMINOPYRIDINE-4-CARBOXYLIC ACID
5fp8	CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 -METHYLTHIOPHEN-2-YLMETHYLAMINOPYRIDINE-4-CARBOXYLIC ACID
5fp9	CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3- AMINOPYRIDINE-4-CARBOXYLIC ACID
5fpa	CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3H, 4H-PYRIDO-3,4-D-PYRIMIDIN-4-ONE
5fpb	CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 2- 1H-PYRAZOL-4-YLOXY-3H,4H-PYRIDO-3,4-D-PYRIMIDIN- 4-ONE

Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

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Cis Peptide Bonds (2, 2)

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