Structure of PDB 5zf8 Chain A Binding Site BS02

Receptor Information
>5zf8 Chain A (length=366) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAEL
RRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGL
IVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPI
IGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKE
QGFGGVTDAIGADHRR
Ligand information
Ligand ID9BO
InChIInChI=1S/C21H27ClO5/c1-12(7-6-8-13(2)15(4)27-16(5)24)9-10-17-20(25)18(11-23)14(3)19(22)21(17)26/h8-9,11,15,25-26H,6-7,10H2,1-5H3/b12-9+,13-8+/t15-/m0/s1
InChIKeyYBGJUDVVSGWLOR-KYXQLXBKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](OC(C)=O)C(C)=CCCC(C)=CCc1c(O)c(Cl)c(C)c(C=O)c1O
OpenEye OEToolkits 2.0.6Cc1c(c(c(c(c1Cl)O)C/C=C(\C)/CC/C=C(\C)/[C@H](C)OC(=O)C)O)C=O
CACTVS 3.385C[C@H](OC(C)=O)/C(C)=C/CC\C(C)=C\Cc1c(O)c(Cl)c(C)c(C=O)c1O
ACDLabs 12.01CC(=O)OC(C)C(C)=[C@H]CCC(=[C@H]Cc1c(c(C=O)c(C)c(Cl)c1O)O)C
OpenEye OEToolkits 2.0.6Cc1c(c(c(c(c1Cl)O)CC=C(C)CCC=C(C)C(C)OC(=O)C)O)C=O
FormulaC21 H27 Cl O5
Name(2S,3E,7E)-9-(3-chloro-5-formyl-2,6-dihydroxy-4-methylphenyl)-3,7-dimethylnona-3,7-dien-2-yl acetate
ChEMBL
DrugBank
ZINC
PDB chain5zf8 Chain A Residue 410 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5zf8 Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		M43 L46 Q47 P52 A55 H56 A59 F98 R136 Y356 L359 T360 G363 P364
Binding residue
(residue number reindexed from 1)		M13 L16 Q17 P22 A25 H26 A29 F68 R106 Y326 L329 T330 G333 P334
Annotation score1
Binding affinityMOAD: ic50=6.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) G119 N145 F149 S215 N217 T218 K255 N284
Catalytic site (residue number reindexed from 1) G89 N115 F119 S185 N187 T188 K225 N254
Enzyme Commision number 1.3.5.2: dihydroorotate dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0004151 dihydroorotase activity
GO:0004152 dihydroorotate dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0106430 dihydroorotate dehydrogenase (quinone) activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0009220 pyrimidine ribonucleotide biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005829 cytosol
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5zf8, PDBe:5zf8, PDBj:5zf8
PDBsum5zf8
PubMed30233375
UniProtQ02127|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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