Structure of PDB 6j3b Chain A

Receptor sequence

>6j3bA (length=366) Species: 9606 (Homo sapiens) [Search protein sequence]

ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAEL
RRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGL
IVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPI
IGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKE
QGFGGVTDAIGADHRR

3D structure

PDB

6j3b A novel series of human dihydroorotate dehydrogenase inhibitors discovered by in vitro screening: inhibition activity and crystallographic binding mode.

Chain

Resolution

1.6 Å

3D
structure

Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Catalytic site (original residue number in PDB)	N145 F149 S215 N217 T218 K255 N284
Catalytic site (residue number reindexed from 1)	N115 F119 S185 N187 T188 K225 N254
Enzyme Commision number	1.3.5.2: dihydroorotate dehydrogenase (quinone).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FMN	A	A96 G97 K100 S120 N145 N212 K255 N284 T285 S305 G306 V333 G334 G335 L355 Y356 T357	A66 G67 K70 S90 N115 N182 K225 N254 T255 S275 G276 V303 G304 G305 L325 Y326 T327
BS02	B5O	A	Y38 M43 L46 P52 A55 H56 A59 T63 R136 Y356 L359 T360 P364	Y8 M13 L16 P22 A25 H26 A29 T33 R106 Y326 L329 T330 P334	MOAD: ic50=171nM

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:6j3b, PDBe:6j3b, PDBj:6j3b
PDBsum	6j3b
PubMed	31087527
UniProt	Q02127\|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

[Back to BioLiP]