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(-) 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 :  1.95
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
    Expression System Plasmid: PET-19B
    Expression System Strain: BL21(DE3)
    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, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL3Ligand/IonCHLORIDE ION
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4ORO1Ligand/IonOROTIC ACID
5U911Ligand/Ion1,5-DIMETHYL-3-OXIDANYL-~{N}-[2,3,5,6-TETRAKIS(FLUORANYL)-4-PHENYL-PHENYL]PYRAZOLE-4-CARBOXAMIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , GLY A:119 , SER A:120 , ASN A:145 , 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:517 , HOH A:574binding site for residue FMN A 401
2AC2SOFTWARELYS 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
3AC3SOFTWAREMET A:43 , LEU A:46 , ALA A:55 , HIS A:56 , ALA A:59 , LEU A:67 , LEU A:68 , VAL A:134 , ARG A:136 , TYR A:356 , THR A:360 , HOH A:536binding site for residue U91 A 403
4AC4SOFTWAREALA A:169 , THR A:172 , LEU A:205 , ASP A:207 , HOH A:522binding site for residue ACT A 404
5AC5SOFTWARELYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:586binding site for residue ACT A 405
6AC6SOFTWAREGLN A:165 , PRO A:204 , HIS A:248 , ARG A:298 , SER A:299binding site for residue CL A 406
7AC7SOFTWAREPRO A:52 , ARG A:136 , HOH A:646binding site for residue CL A 407

(-) SS Bonds  (0, 0)

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

(-) 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 5MVD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MVD)

(-) 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:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 5mvd A  34 DERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    43        53        63     || 78        88        98       108       118       128       138       148       158       168       178       188       198       208       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        
                                                              69|                                                                                                                                          216|                                                                                                                                                                         
                                                               75                                                                                                                                           227
   Legend:   → Mismatch (orange background)
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  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 5MVD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:131 - Pro A:132   [ RasMol ]  
    Gly A:119 - Ser A:120   [ RasMol ]  
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  5mvd
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  PYRD_HUMAN | Q02127
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 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 5mvc

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