3HB5 - JenaLib

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Title :   BINARY AND TERNARY CRYSTAL STRUCTURES OF A NOVEL INHIBITOR OF 17 BETA-HSD TYPE 1: A LEAD COMPOUND FOR BREAST CANCER THERAPY

Authors :   M. Mazumdar, S. -X. Lin

Date :   04 May 09 (Deposition) - 15 Dec 09 (Release) - 15 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : X
Biol. Unit 1: X  (2x)

Keywords :   17Beta-Hsd1, Cytoplasm, Lipid Synthesis, Nadp, Oxidoreductase, Polymorphism, Steroid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Mazumdar, D. Fournier, D. W. Zhu, C. Cadot, D. Poirier, S. X. Lin
Binary And Ternary Crystal Structure Analyses Of A Novel Inhibitor With 17Beta-Hsd Type 1: A Lead Compound For Breast Cancer Therapy.
Biochem. J. V. 424 357 2009
PubMed-ID: 19929851 | Reference-DOI: 10.1042/BJ20091020
(for further references see the PDB file header)

Molecule 1 - ESTRADIOL 17-BETA-DEHYDROGENASE 1
	Chains	:	X
	EC Number	:	1.1.1.62
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	PROTEIN PURIFIED FROM HUMAN PLACENTA
	Synonym	:	17-BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1, 17- BETA-HSD 1, PLACENTAL 17-BETA-HYDROXYSTEROID DEHYDROGENASE, 20 ALPHA-HYDROXYSTEROID DEHYDROGENASE, 20-ALPHA-HSD, E2DH

		1
Asymmetric Unit	:	X
Biological Unit 1 (2x)	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	E2B	1	Ligand/Ion	3-{[(9BETA,14BETA,16ALPHA,17ALPHA)-3,17-DIHYDROXYESTRA-1,3,5(10)-TRIEN-16-YL]METHYL}BENZAMIDE
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	E2B	2	Ligand/Ion	3-{[(9BETA,14BETA,16ALPHA,17ALPHA)-3,17-DIHYDROXYESTRA-1,3,5(10)-TRIEN-16-YL]METHYL}BENZAMIDE
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY X:9 , CYS X:10 , SER X:11 , SER X:12 , ILE X:14 , GLY X:15 , THR X:35 , LEU X:36 , ARG X:37 , LEU X:64 , ASP X:65 , VAL X:66 , ARG X:67 , ASN X:90 , ALA X:91 , GLY X:92 , THR X:140 , GLY X:141 , TYR X:155 , LYS X:159 , CYS X:185 , GLY X:186 , VAL X:188 , THR X:190 , PHE X:192 , HOH X:344 , HOH X:370 , HOH X:404 , HOH X:419	BINDING SITE FOR RESIDUE NAP X 360

(no "SS Bond" information available for 3HB5)

(no "Cis Peptide Bond" information available for 3HB5)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006951	A	238	V	DHB1_HUMAN	Polymorphism	147402365	X	A	237	V

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006951	A	238	V	DHB1_HUMAN	Polymorphism	147402365	X	A	237	V

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHB1_HUMAN	143-171	1	X:142-170

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHB1_HUMAN	143-171	2	X:142-170

(no "Exon" information available for 3HB5)

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 X from PDB  Type:PROTEIN  Length:284
 aligned with DHB1_HUMAN | P14061 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:284
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    
           DHB1_HUMAN     2 ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKTQGRLWEAARALACPPGSLETLQLDVRDSKSVAAARERVTEGRVDVLVCNAGLGLLGPLEALGEDAVASVLDVNVVGTVRMLQAFLPDMKRRGSGRVLVTGSVGGLMGLPFNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTAFMEKVLGSPEEVLDRTDIHTFHRFYQYLAHSKQVFREAAQNPEEVAEVFLTALRAPKPTLRYFTTERFLPLLRMRLDDPSGSNYVTAMHREVF 285
               SCOP domains d3hb5x_ X: Human estrogenic 17beta-hydroxysteroid dehydrogenase                                                                                                                                                                                                                              SCOP domains
               CATH domains 3hb5X00 X:1-284 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh.......eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eee....hhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: X:142-170    ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hb5 X   1 ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKTQGRLWEAARALACPPGSLETLQLDVRDSKSVAAARERVTEGRVDVLVCNAGLGLLGPLEALGEDAVASVLDVNVVGTVRMLQAFLPDMKRRGSGRVLVTGSVGGLMGLPFNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTAFMEKVLGSPEEVLDRTDIHTFHRFYQYLAHSKQVFREAAQNPEEVAEVFLTALRAPKPTLRYFTTERFLPLLRMRLDDPSGSNYVTAMHREVF 284
                                    10        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

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 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: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Human estrogenic 17beta-hydroxysteroid dehydrogenase (22)

Human (Homo sapiens) [TaxId: 9606] (22)

d3hb5x_

Asymmetric 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: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

3hb5X00

X:1-284

(no "Pfam Domain" information available for 3HB5)

Asymmetric Unit(hide GO term definitions)

Chain X (DHB1_HUMAN | P14061)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004303	estradiol 17-beta-dehydrogenase activity	Catalysis of the reaction: estradiol-17-beta + NADP+ = estrone + NADPH + H+.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0047035	testosterone dehydrogenase (NAD+) activity	Catalysis of the reaction: testosterone + NAD+ = androst-4-ene-3,17-dione + NADH.
biological process
	GO:0060348	bone development	The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
	GO:0071248	cellular response to metal 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 metal ion stimulus.
	GO:0006703	estrogen biosynthetic process	The chemical reactions and pathways resulting in the formation of estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
	GO:0008210	estrogen metabolic process	The chemical reactions and pathways involving estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
	GO:0061370	testosterone biosynthetic process	The chemical reactions and pathways resulting in the formation of testosterone, an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4 C-5.
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:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

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	3hb5
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Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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