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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE WITH ML390
 
Authors :  T. A. Lewis, D. B. Sykes, J. M. Law, B. Munoz, D. T. Scadden, J. K. Rustigue M. C. Nonato, S. L. Schreiber
Date :  31 May 16  (Deposition) - 12 Oct 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Alpha/Beta Barrel, Inhibitor, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Lewis, D. B. Sykes, J. M. Law, B. Munoz, J. K. Rustiguel, M. C. Nonato, D. T. Scadden, S. L. Schreiber
Development Of Ml390: A Human Dhodh Inhibitor That Induces Differentiation In Acute Myeloid Leukemia.
Acs Med Chem Lett V. 7 1112 2016
PubMed-ID: 27994748  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00316

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 29-395
    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  (7, 11)

Asymmetric/Biological Unit (7, 11)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3FNR1Ligand/Ion1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
4GOL1Ligand/IonGLYCEROL
5MLJ1Ligand/Ion~{N}-[3-OXIDANYLIDENE-3-[[(1~{R})-1,2,3,4-TETRAHYDRONAPHTHALEN-1-YL]AMINO]PROPYL]-4-(TRIFLUOROMETHYLOXY)BENZAMIDE
6ORO1Ligand/IonOROTIC ACID
7SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA 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:401 , HOH A:534 , HOH A:576binding site for residue FNR A 400
02AC2SOFTWARELYS 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 , FNR A:400binding site for residue ORO A 401
03AC3SOFTWAREMET A:43 , LEU A:46 , GLN A:47 , LEU A:50 , PRO A:52 , ALA A:55 , HIS A:56 , LEU A:58 , ALA A:59 , PHE A:62 , PHE A:98 , VAL A:134 , ARG A:136 , TYR A:356 , THR A:360 , PHE A:361binding site for residue MLJ A 402
04AC4SOFTWAREARG A:245 , VAL A:247 , HIS A:248 , HOH A:550binding site for residue SO4 A 403
05AC5SOFTWAREARG A:249 , HOH A:546binding site for residue SO4 A 404
06AC6SOFTWAREGLN A:168 , ALA A:169 , THR A:172 , LEU A:205 , ALA A:206 , ASP A:207 , HOH A:511 , HOH A:569 , HOH A:581binding site for residue ACT A 405
07AC7SOFTWARELYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:552 , HOH A:561binding site for residue ACT A 406
08AC8SOFTWAREARG A:160 , HOH A:577 , HOH A:635 , HOH A:637 , HOH A:689binding site for residue ACT A 407
09AC9SOFTWAREGLN A:165 , HIS A:248 , ARG A:298 , SER A:299 , HOH A:659binding site for residue CL A 408
10AD1SOFTWAREARG A:347 , GLN A:381 , HOH A:523binding site for residue CL A 409
11AD2SOFTWARELYS A:167 , LYS A:227 , ARG A:231 , HOH A:520binding site for residue GOL A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K9C)

(-) 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 5K9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K9C)

(-) Exons   (0, 0)

(no "Exon" information available for 5K9C)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k9c A  35 ERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   ||  231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391     
                                                                                                                                                                                                                 218|                                                                                                                                                                          
                                                                                                                                                                                                                  226
   Legend:   → Mismatch (orange background)
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  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 5K9C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K9C)

(-) 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 ]  
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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 5k9d 5mut 5mvc 5mvd

(-) Related Entries Specified in the PDB File

5k9d