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Asym./Biol. Unit (Jmol Viewer)

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Title :   DISCOVERY OF NOVEL URACIL DERIVATIVES AS POTENT HUMAN DUTPASE INHIBITORS

Authors :   K. T. Chong, H. Miyakoshi, S. Miyahara, M. Fukuoka

Date :   25 Nov 10 (Deposition) - 08 Dec 10 (Release) - 30 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Hydrolase, Magnesium Binding, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Miyakoshi, S. Miyahara, T. Yokogawa, K. T. Chong, J. Taguchi, K. Endoh, W. Yano, T. Wakasa, H. Ueno, Y. Takao, M. Nomura, S. Shuto, H. Nagasawa, M. Fukuoka
Synthesis And Discovery Of N-Carbonylpyrrolidine- Or N-Sulfonylpyrrolidine-Containing Uracil Derivatives As Potent Human Deoxyuridine Triphosphatase Inhibitors
J. Med. Chem. V. 55 2960 2012
PubMed-ID: 22404301 | Reference-DOI: 10.1021/JM201627N

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
	Chains	:	A, B, C
	EC Number	:	3.6.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET19B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DUT-N, DUTPASE, DUTP PYROPHOSPHATASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MKH	3	Ligand/Ion	1-[3-({(2R)-2-[HYDROXY(DIPHENYL)METHYL]PYRROLIDIN-1-YL}SULFONYL)PROPYL]PYRIMIDINE-2,4(1H,3H)-DIONE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:98 , GLY A:99 , VAL A:100 , TYR A:105 , VAL A:109 , GLY A:110 , VAL A:112 , GLN A:146 , HOH A:173 , HOH A:195 , HOH A:222 , SER C:86 , ALA C:90	BINDING SITE FOR RESIDUE MKH A 165
2	AC2	SOFTWARE	GLU A:135 , GLU B:135 , HOH B:168 , GLU C:135	BINDING SITE FOR RESIDUE MG A 166
3	AC3	SOFTWARE	SER A:86 , LYS B:67 , ALA B:98 , GLY B:99 , VAL B:100 , TYR B:105 , VAL B:109 , GLY B:110 , VAL B:112 , HOH B:172 , HOH B:206 , HOH B:271	BINDING SITE FOR RESIDUE MKH B 165
4	AC4	SOFTWARE	HIS A:34 , HIS B:34 , HIS C:34	BINDING SITE FOR RESIDUE MG B 166
5	AC5	SOFTWARE	SER B:86 , ALA B:90 , VAL C:65 , GLY C:99 , VAL C:100 , TYR C:105 , VAL C:109 , GLY C:110 , VAL C:112 , HOH C:167 , HOH C:293	BINDING SITE FOR RESIDUE MKH C 165

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

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

(no "SAP(SNP)/Variant" information available for 3ARA)

(no "PROSITE Motif" information available for 3ARA)

Asymmetric/Biological Unit (6, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000331200	1b	ENSE00001487133	chr15:48623621-48623992	372	DUT_HUMAN	1-94	94	0	-	-
1.2b	ENST00000331200	2b	ENSE00001789447	chr15:48624465-48624603	139	DUT_HUMAN	94-140	47	3	A:24-52 B:24-52 C:24-52	29 29 29
1.3	ENST00000331200	3	ENSE00000686853	chr15:48626614-48626705	92	DUT_HUMAN	140-171	32	3	A:52-83 B:52-83 C:52-83	32 32 32
1.4	ENST00000331200	4	ENSE00000686856	chr15:48628243-48628287	45	DUT_HUMAN	171-186	16	3	A:83-98 B:83-98 C:83-98	16 16 16
1.5	ENST00000331200	5	ENSE00000686860	chr15:48633486-48633560	75	DUT_HUMAN	186-211	26	3	A:98-123 B:98-123 C:98-123	26 26 26
1.6	ENST00000331200	6	ENSE00000884477	chr15:48633712-48633782	71	DUT_HUMAN	211-234	24	3	A:123-146 B:123-146 C:123-146	24 24 24
1.7b	ENST00000331200	7b	ENSE00001030201	chr15:48634219-48635570	1352	DUT_HUMAN	235-252	18	3	A:147-148 B:147-148 C:147-148	2 2 2

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:125
 aligned with DUT_HUMAN | P33316 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:125
                                   121       131       141       151       161       171       181       191       201       211       221       231     
            DUT_HUMAN   112 MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQAL 236
               SCOP domains d3araa_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.................eeee....eee...eeeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:24-52      ------------------------------Exon 1.4        ------------------------Exon 1.6  PDB: A:123-1461. Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: A:52-83          --------------Exon 1.5  PDB: A:98-123   ------------------------- Transcript 1 (2)
                 3ara A  24 MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQAL 148
                                    33        43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with DUT_HUMAN | P33316 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:125
                                   121       131       141       151       161       171       181       191       201       211       221       231     
            DUT_HUMAN   112 MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQAL 236
               SCOP domains d3arab_ B: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................eeee....eee...eeeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:24-52      ------------------------------Exon 1.4        ------------------------Exon 1.6  PDB: B:123-1461. Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: B:52-83          --------------Exon 1.5  PDB: B:98-123   ------------------------- Transcript 1 (2)
                 3ara B  24 MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQAL 148
                                    33        43        53        63        73        83        93       103       113       123       133       143

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with DUT_HUMAN | P33316 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:125
                                   121       131       141       151       161       171       181       191       201       211       221       231     
            DUT_HUMAN   112 MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQAL 236
               SCOP domains d3arac_ C: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.................eeee....eee...eeeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: C:24-52      ------------------------------Exon 1.4        ------------------------Exon 1.6  PDB: C:123-1461. Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: C:52-83          --------------Exon 1.5  PDB: C:98-123   ------------------------- Transcript 1 (2)
                 3ara C  24 MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQAL 148
                                    33        43        53        63        73        83        93       103       113       123       133       143

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: dUTPase-like (122)

Family: automated matches (51)

Protein domain: automated matches (51)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d3araa_	A:
1b	d3arab_	B:
1c	d3arac_	C:

(no "CATH Domain" information available for 3ARA)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DUT_HUMAN | P33316)

molecular function
	GO:0004170	dUTP diphosphatase activity	Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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).
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006226	dUMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
	GO:0046081	dUTP catabolic process	The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
	GO:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	GO:0046134	pyrimidine nucleoside biosynthetic process	The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
cellular component
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ara)

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	3ara
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	DUT_HUMAN \| P33316
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	3.6.1.23
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UniProtKB/Swiss-Prot
	DUT_HUMAN \| P33316	:	1q5h 1q5u 2hqu 3arn 3ehw 4mz5 4mz6

1q5h	THE SAME PROTEIN COMPLEXED WITH DEOXYURIDINE-5'-DIPHOSPHATE
2hqu	THE SAME PROTEIN COMPLEXED WITH 2'-DEOXYURIDINE 5'-ALPHA, BETA-IMIDO-TRIPHOSPHATE
3ehw	THE SAME PROTEIN COMPLEXED WITH 2'-DEOXYURIDINE 5'-ALPHA, BETA-IMIDO-TRIPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (6, 18)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File