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Asym./Biol. Unit (Jmol Viewer)

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

Title :   N-BENZYL-INDOLO CARBOXYLIC ACIDS: DESIGN AND SYNTHESIS OF POTENT AND SELECTIVE ADIPOCYTE FATTY-ACID BINDING PROTEIN (A-FABP) INHIBITORS

Authors :   T. Barf, K. Hammer, F. Lehmann, S. Haile, E. Axen, C. Medina, J. Uppenberg, S. Svensson, L. Rondahl, T. Lundb Ck

Date :   08 Jan 09 (Deposition) - 10 Mar 09 (Release) - 31 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.16

Chains :   Asym./Biol. Unit : A

Keywords :   Selective Adipocyte Fatty-Acid Binding Protein (A-Fabp) Inhibitors, Cytoplasm, Lipid-Binding, Nucleus, Phosphoprotein, Polymorphism, Transport, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Barf, F. Lehmann, K. Hammer, S. Haile, E. Axen, C. Medina, J. Uppenberg, S. Svensson, L. Rondahl, T. Lundback
N-Benzyl-Indolo Carboxylic Acids: Design And Synthesis Of Potent And Selective Adipocyte Fatty-Acid Binding Protein (A-Fabp) Inhibitors.
Bioorg. Med. Chem. Lett. V. 19 1745 2009
PubMed-ID: 19217286 | Reference-DOI: 10.1016/J.BMCL.2009.01.084
(for further references see the PDB file header)

Molecule 1 - FATTY ACID-BINDING PROTEIN, ADIPOCYTE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	FABP4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	A-FABP, AFABP, FATTY ACID-BINDING PROTEIN 4, ADIPOCYTE LIPID-BINDING PROTEIN, ALBP

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	F8A	1	Ligand/Ion	9-[2-(TRIFLUOROMETHYL)BENZYL]-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-8-CARBOXYLIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:16 , ALA A:33 , ALA A:36 , PRO A:38 , SER A:53 , SER A:55 , PHE A:57 , LYS A:58 , THR A:60 , ASP A:76 , ARG A:78 , CYS A:117 , ARG A:126 , TYR A:128 , HOH A:158 , HOH A:236	BINDING SITE FOR RESIDUE F8A A 501

(no "SS Bond" information available for 3FR4)

(no "Cis Peptide Bond" information available for 3FR4)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036320	E	23	D	FABP4_HUMAN	Unclassified	---	A	E	22	D
2	CancerSNP	VAR_FABP4_HUMAN_CCDS6230_1_01 *	E	23	D	FABP4_HUMAN	Disease (Breast cancer)	---	A	E	22	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	FABP4_HUMAN	7-24	1	A:6-23

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000256104	1a	ENSE00002139695	chr8:82395498-82395330	169	FABP4_HUMAN	1-25	25	1	A:1-24	24
1.2a	ENST00000256104	2a	ENSE00000698161	chr8:82392833-82392661	173	FABP4_HUMAN	25-82	58	1	A:24-81	58
1.3b	ENST00000256104	3b	ENSE00000698160	chr8:82391750-82391649	102	FABP4_HUMAN	83-116	34	1	A:82-115	34
1.4d	ENST00000256104	4d	ENSE00000795008	chr8:82391150-82390654	497	FABP4_HUMAN	117-132	16	1	A:116-131	16

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
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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with FABP4_HUMAN | P15090 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 
          FABP4_HUMAN     2 CDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVMKGVTSTRVYERA 132
               SCOP domains d3fr4a_ A: Adipocyte lipid-binding protein, ALBP                                                                                    SCOP domains
               CATH domains 3fr4A00 A:1-131  [code=2.40.128.20, no name defined]                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhhh.hhhhhhhhhhh..eeeeeee..eeeeeee.....eeeeee....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------D------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------D------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----FABP  PDB: A:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-24  ---------------------------------------------------------Exon 1.3b  PDB: A:82-115          Exon 1.4d        Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2a  PDB: A:24-81 UniProt: 25-82                    -------------------------------------------------- Transcript 1 (2)
                 3fr4 A   1 CDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVMKGVTSTRVYERA 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Fatty acid binding protein-like (183)

Protein domain: Adipocyte lipid-binding protein, ALBP (34)

Human (Homo sapiens) [TaxId: 9606] (15)

d3fr4a_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Human (Homo sapiens) (91)

3fr4A00

A:1-131

(no "Pfam Domain" information available for 3FR4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FABP4_HUMAN | P15090)

molecular function
	GO:0005504	fatty acid binding	Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0050873	brown fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
	GO:0071285	cellular response to lithium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus.
	GO:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	GO:0001816	cytokine production	The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	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.
	GO:0019433	triglyceride catabolic process	The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
	GO:0050872	white fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a white adipocyte, an animal connective tissue cell involved in energy storage. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 1)

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