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(-) Description

Title :  DUAL BINDING MODE OF A NOVEL SERIES OF DHODH INHIBITORS
 
Authors :  R. Baumgartner, M. Walloschek, M. Karlik, A. Gotschlich, S. Tasler, J. Mies, J. Leban
Date :  27 Jul 05  (Deposition) - 16 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Dihydroorotate Dehydrogenase Inhibitor, Dual Binding Mode, Virtual High-Throughput Screening, Rheumatoid Arthritis Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Baumgartner, M. Walloschek, M. Kralik, A. Gotschlich, S. Tasler, J. Mies, J. Leban
Dual Binding Mode Of A Novel Series Of Dhodh Inhibitors.
J. Med. Chem. V. 49 1239 2006
PubMed-ID: 16480261  |  Reference-DOI: 10.1021/JM0506975

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
    ChainsA
    EC Number1.3.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism CommonHOMO SAPIENS
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDIHYDROOROTATE OXIDASE, DHODEHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
13FT1Ligand/Ion2-({[3-FLUORO-3'-(TRIFLUOROMETHOXY)BIPHENYL-4-YL]AMINO}CARBONYL)CYCLOPENT-1-ENE-1-CARBOXYLIC ACID
2ACT1Ligand/IonACETATE ION
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4ORO1Ligand/IonOROTIC ACID
5SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:245 , VAL A:247 , HIS A:248 , HOH A:2190 , HOH A:2191BINDING SITE FOR RESIDUE SO4 A1397
2AC2SOFTWARELYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:2192BINDING SITE FOR RESIDUE ACT A1398
3AC3SOFTWAREALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , GLY A:119 , SER A:120 , ASN A:145 , TYR A:147 , ASN A:181 , ASN A:212 , LYS A:255 , THR A:283 , ASN A:284 , THR A:285 , SER A:305 , GLY A:306 , LEU A:309 , VAL A:333 , GLY A:334 , GLY A:335 , LEU A:355 , TYR A:356 , THR A:357 , ORO A:1400 , HOH A:2170 , HOH A:2193BINDING SITE FOR RESIDUE FMN A1399
4AC4SOFTWARELYS A:100 , ASN A:145 , TYR A:147 , GLY A:148 , PHE A:149 , ASN A:212 , SER A:215 , ASN A:217 , ASN A:284 , THR A:285 , FMN A:1399BINDING SITE FOR RESIDUE ORO A1400
5AC5SOFTWARETYR A:38 , LEU A:42 , LEU A:46 , GLN A:47 , HIS A:56 , ALA A:59 , PHE A:62 , LEU A:67 , LEU A:68 , PHE A:98 , ARG A:136 , TYR A:356 , LEU A:359 , THR A:360 , PRO A:364 , HOH A:2062BINDING SITE FOR RESIDUE 3FT A1401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BXV)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:119 -Ser A:120
2Arg A:131 -Pro A:132
3Val A:282 -Thr A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_062413R135CPYRD_HUMANDisease (POADS)201230446AR136C
2UniProtVAR_062414G152RPYRD_HUMANDisease (POADS)267606766AG153R
3UniProtVAR_062415R199CPYRD_HUMANDisease (POADS)267606769AR200C
4UniProtVAR_062416G202APYRD_HUMANDisease (POADS)267606767AG203A
5UniProtVAR_062417G202DPYRD_HUMANDisease (POADS)267606767AG203D
6UniProtVAR_062418R244WPYRD_HUMANDisease (POADS)267606768AR245W
7UniProtVAR_062419T284IPYRD_HUMANDisease (POADS)  ---AT285I
8UniProtVAR_062420R346WPYRD_HUMANDisease (POADS)201947120AR347W
9UniProtVAR_062421D392GPYRD_HUMANDisease (POADS)779076692AD393G

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHODEHASE_1PS00911 Dihydroorotate dehydrogenase signature 1.PYRD_HUMAN113-132  1A:114-133
2DHODEHASE_2PS00912 Dihydroorotate dehydrogenase signature 2.PYRD_HUMAN329-349  1A:330-350

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002192401ENSE00001420633chr16:72042643-7204268442PYRD_HUMAN1-770--
1.2ENST000002192402ENSE00000799143chr16:72045949-72046161213PYRD_HUMAN8-78711A:30-79 (gaps)50
1.3ENST000002192403ENSE00000692663chr16:72048372-72048571200PYRD_HUMAN79-145671A:80-14667
1.4ENST000002192404ENSE00000692662chr16:72050923-7205100583PYRD_HUMAN145-173291A:146-17429
1.5ENST000002192405ENSE00000692661chr16:72055023-72055210188PYRD_HUMAN173-235631A:174-236 (gaps)63
1.6ENST000002192406ENSE00000692660chr16:72056261-72056374114PYRD_HUMAN236-273381A:237-27438
1.7ENST000002192407ENSE00001718063chr16:72057064-72057217154PYRD_HUMAN274-325521A:275-32652
1.8ENST000002192408ENSE00001662402chr16:72057373-72057532160PYRD_HUMAN325-378541A:326-37954
1.9ENST000002192409ENSE00001737850chr16:72058044-72058954911PYRD_HUMAN378-395181A:379-39618

(-) Sequences/Alignments

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:360
 aligned with PYRD_HUMAN | Q02127 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:367
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       
           PYRD_HUMAN    29 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 395
               SCOP domains d2bxva_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2bxvA00 A:30-396 Aldolase class I                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....---...hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.........----hhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------C----------------R----------------------------------------------C--A-----------------------------------------W---------------------------------------I-------------------------------------------------------------W---------------------------------------------G--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------DHODEHASE_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          ---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:30-79 (gaps) UniProt: 8-78       Exon 1.3  PDB: A:80-146 UniProt: 79-145                            ---------------------------Exon 1.5  PDB: A:174-236 (gaps) UniProt: 173-235               Exon 1.6  PDB: A:237-274              Exon 1.7  PDB: A:275-326 UniProt: 274-325           ----------------------------------------------------Exon 1.9           Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:146-174     -------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:326-379 UniProt: 325-378             ----------------- Transcript 1 (2)
                 2bxv A  30 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLP---FQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGL----GKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    39        49        59        69   |    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 |    |229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       
                                                                  69  73                                                                                                                                                 221  226                                                                                                                                                                          

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BXV)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYRD_HUMAN | Q02127)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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:0004152    dihydroorotate dehydrogenase activity    Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0048039    ubiquinone binding    Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    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).
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0090140    regulation of mitochondrial fission    Any process that modulates the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:0031000    response to caffeine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRD_HUMAN | Q021271d3g 1d3h 2b0m 2fpt 2fpv 2fpy 2fqi 2prh 2prl 2prm 2wv8 3f1q 3fj6 3fjl 3g0u 3g0x 3kvj 3kvk 3kvl 3kvm 3u2o 3w7r 3zws 3zwt 4igh 4jgd 4js3 4jts 4jtt 4jtu 4ls0 4ls1 4ls2 4oqv 4rk8 4rka 4rli 4rr4 4ylw 4zl1 4zmg 5h2z 5hin 5hqe 5k9c 5k9d 5mut 5mvc 5mvd

(-) Related Entries Specified in the PDB File

1d3g HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH BREQUINAR ANALOG
1d3h HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATIVE AGENT A771726