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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.

Authors :   J. Sandmark, M. Althage, G. M. K. Andersson, T. Antonsson, S. Blaho, C. B J. Bostrom, Y. Chen, A. Dahlen, P. O. Eriksson, E. Evertsson, T. Fex, O. Fjellstrom, D. Gustafsson, C. Hallberg, R. Hicks, E. Jarkvist, C. J I. Kalies, D. Kang, B. Svalstedt Karlsson, F. Kartberg, A. Legnehed, A. M. Lindqvist, S. A. Martinsson, A. Moberg, A. U. Petersson, M. Ridde A. Thelin, A. Tigerstrom, J. Vinblad, B. Xu, W. Knecht

Date :   28 Jun 13 (Deposition) - 16 Jul 14 (Release) - 16 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Cardiovascular Disease, Drug Discovery, Optical Biosensors (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Sandmark, M. Althage, G. M. K. Andersson, T. Antonsson, S. Blaho, C. Bodin, J. Bostrom, Y. Chen, A. Dahlen, P. O. Eriksson, E. Evertsson, T. Fex, O. Fjellstrom, D. Gustafsson, C. Hallberg, R. Hicks, E. Jarkvist, C. Johansson, I. Kalies, D. Kang, B. Svalstedt Karlsson F. Kartberg, A. Legnehed, A. M. Lindqvist, S. A. Martinsson, A. Moberg A. U. Petersson, M. Ridderstrom, A. Thelin, A. Tigerstrom, J. Vinblad B. Xu, W. Knecht
Small Molecules Used To Decipher The Pathophysiological Roles Of The Kringle Domains Kiv-7, - 10 And Kv Of Apolipoprotein(A)
To Be Published
PubMed: search

Molecule 1 - APOLIPOPROTEIN(A)
	Chains	:	A
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	KOMAGATAELLA PASTORIS
	Expression System Plasmid	:	PPICZALPHAC
	Expression System Strain	:	X-33
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	KRINGLE DOMAIN V, RESIDUES 4227-4307
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	APO(A), LP(A)

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CPF	1	Ligand/Ion	1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:3 , SER A:34 , THR A:35 , ASP A:55 , ASP A:57 , ILE A:58 , ASN A:59 , TRP A:62 , TYR A:64 , LEU A:71 , PHE A:72	BINDING SITE FOR RESIDUE CPF A1081
2	AC2	SOFTWARE	ASP A:0 , TYR A:9 , LYS A:12 , LYS A:13	BINDING SITE FOR RESIDUE SO4 A1082

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	A:80
2	A:22	-	A:63
3	A:51	-	A:75

Asymmetric/Biological Unit

No.	Residues
1	Glu A:29	-	Pro A:30

(no "SAP(SNP)/Variant" information available for 4BVV)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KRINGLE_2	PS50070	Kringle domain profile.	APOA_HUMAN	27-105 141-219 255-333 369-447 483-561 597-675 711-789 825-903 939-1017 1053-1131 1167-1245 1281-1359 1395-1473 1509-1587 1623-1701 1737-1815 1851-1929 1965-2043 2079-2157 2193-2271 2307-2385 2421-2499 2535-2613 2649-2727 2763-2841 2877-2955 2991-3069 3105-3183 3219-3297 3333-3411 3447-3525 3561-3639 3675-3753 3781-3859 3895-3973 4009-4087 4123-4201 4227-4307	1	- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A:0-80
2	KRINGLE_1	PS00021	Kringle domain signature.	APOA_HUMAN	76-88 190-202 304-316 418-430 532-544 646-658 760-772 874-886 988-1000 1102-1114 1216-1228 1330-1342 1444-1456 1558-1570 1672-1684 1786-1798 1900-1912 2014-2026 2128-2140 2242-2254 2356-2368 2470-2482 2584-2596 2698-2710 2812-2824 2926-2938 3040-3052 3154-3166 3268-3280 3382-3394 3496-3508 3610-3622 3724-3736 3830-3842 3944-3956 4058-4070 4172-4184 4277-4290	1	- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A:50-63

(no "Exon" information available for 4BVV)

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:81
 aligned with APOA_HUMAN | P08519 from UniProtKB/Swiss-Prot  Length:4548

    Alignment length:81
                                  4236      4246      4256      4266      4276      4286      4296      4306 
          APOA_HUMAN   4227 DCMFGNGKGYRGKKATTVTGTPCQEWAAQEPHRHSTFIPGTNKWAGLEKNYCRNPDGDINGPWCYTMNPRKLFDYCDIPLC 4307
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................................eee.......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) KRINGLE_2  PDB: A:0-80 UniProt: 4227-4307                                         PROSITE (1)
                PROSITE (2) --------------------------------------------------KRINGLE_1     ----------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------- Transcript
                4bvv A    0 DCMFGNGKGYRGKKATTVTGTPCQEWAAQEPHRHSTFIPGTNKWAGLEKNYCRNPDGDINGPWCYTMNPRKLFDYCDIPLC   80
                                     9        19        29        39        49        59        69        79

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

(no "SCOP Domain" information available for 4BVV)

(no "CATH Domain" information available for 4BVV)

(no "Pfam Domain" information available for 4BVV)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (APOA_HUMAN | P08519)

molecular function
	GO:0034185	apolipoprotein binding	Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex.
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	GO:0001968	fibronectin binding	Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0008015	blood circulation	The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0006869	lipid transport	The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0042157	lipoprotein metabolic process	The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0034358	plasma lipoprotein particle	A spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Plasma lipoprotein particles transport lipids, which are non-covalently associated with the particles, in the blood or lymph.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:29 - Pro A:30	[ RasMol ]

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Access by PDB/NDB ID
	4bvv
		Family and Domain Information	:	ProDom \| SYSTERS
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	APOA_HUMAN \| P08519
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	3.4.21.-
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		Domain Information	:	XDom
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	APOA_HUMAN \| P08519
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UniProtKB/Swiss-Prot
	APOA_HUMAN \| P08519	:	1i71 1jfn 1kiv 2feb 3kiv 4bv5 4bv7 4bvc 4bvd 4bvw 4kiv

4bv5	IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bv7	IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvc	IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvd	IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvw	IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.

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Ligands, Modified Residues, Ions (2, 2)

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SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

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