Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF POTENT HUMAN DIHYDROOROTATE DEHYDROGENASE INHIBITORS BASED ON HYDROXYLATED AZOLE SCAFFOLDS
 
Authors :  P. Goyal, M. Andersson, A. C. Moritzer, S. Sainas, A. C. Pippione, D. Bos Kadaraghi, M. Lolli, R. Friemann
Date :  16 Jan 17  (Deposition) - 08 Mar 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Dhodh, Human Dhodh, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sainas, A. C. Pippione, M. Giorgis, E. Lupino, P. Goyal, C. Ramondetti, B. Buccinna, M. Piccinini, R. C. Braga, C. H. Andrade, M. Andersson, A. C. Moritzer, R. Friemann, S. Mensa, S. Al-Kadaraghi, D. Boschi, M. L. Lolli
Design, Synthesis, Biological Evaluation And X-Ray Structural Studies Of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based On Hydroxylated Azole Scaffolds.
Eur J Med Chem V. 129 287 2017
PubMed-ID: 28235702  |  Reference-DOI: 10.1016/J.EJMECH.2017.02.017

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-19B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DHODH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DHODEHASE,DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL5Ligand/IonCHLORIDE ION
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4ORO1Ligand/IonOROTIC ACID
5Y9B1Ligand/Ion4-OXIDANYL-~{N}-[2,3,5,6-TETRAKIS(FLUORANYL)-4-PHENYL-PHENYL]-1,2,5-THIADIAZOLE-3-CARBOXAMIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , 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:402 , HOH A:521 , HOH A:560binding site for residue FMN A 401
02AC2SOFTWARELYS A:100 , ASN A:145 , TYR A:147 , GLY A:148 , PHE A:149 , ASN A:212 , SER A:215 , PRO A:216 , ASN A:284 , THR A:285 , FMN A:401binding site for residue ORO A 402
03AC3SOFTWAREMET A:43 , LEU A:46 , GLN A:47 , PRO A:52 , ALA A:55 , HIS A:56 , ALA A:59 , LEU A:67 , LEU A:68 , ARG A:136 , LEU A:359 , THR A:360 , PRO A:364 , HOH A:510 , HOH A:700binding site for residue Y9B A 403
04AC4SOFTWARELYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:629binding site for residue ACT A 404
05AC5SOFTWAREALA A:169 , THR A:172 , LEU A:205 , ASP A:207 , HOH A:551 , HOH A:675binding site for residue ACT A 405
06AC6SOFTWAREARG A:245 , GLY A:302 , HOH A:618 , HOH A:737binding site for residue CL A 406
07AC7SOFTWAREARG A:136binding site for residue CL A 407
08AC8SOFTWAREGLN A:165 , HIS A:248 , ARG A:298 , SER A:299binding site for residue CL A 408
09AC9SOFTWAREGLN A:126 , GLY A:128 , HOH A:572 , HOH A:728binding site for residue CL A 409
10AD1SOFTWAREARG A:200 , HOH A:735binding site for residue CL A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MVC)

(-) 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  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MVC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MVC)

(-) Exons   (0, 0)

(no "Exon" information available for 5MVC)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhheee..eee...eee.........hhhhhhhhh..eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvc A  32 TGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    41        51        61       |74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 ||    234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394  
                                                                69|                                                                                                                                            216|                                                                                                                                                                         
                                                                 73                                                                                                                                             227
   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  (0, 0)

(no "SCOP Domain" information available for 5MVC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MVC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MVC)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    Y9B  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:131 - Pro A:132   [ RasMol ]  
    Gly A:119 - Ser A:120   [ RasMol ]  
    Val A:282 - Thr A:283   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5mvc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRD_HUMAN | Q02127
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.3.5.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PYRD_HUMAN | Q02127
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PYRD_HUMAN | Q02127: 1d3g 1d3h 2b0m 2bxv 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 5mvd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MVC)