Structure of PDB 3kvk Chain A

Receptor sequence

>3kvkA (length=364) Species: 9606 (Homo sapiens) [Search protein sequence]

GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVR
VLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRP
RVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNL
GKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRR
LLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIV
TNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIG
VGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQG
FGGVTDAIGADHRR

3D structure

PDB

3kvk Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures.

Chain

Resolution

2.05 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	G119 N145 F149 S215 N217 T218 K255 N284
Catalytic site (residue number reindexed from 1)	G87 N113 F117 S183 N185 T186 K223 N252
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 S120 N145 N181 N212 K255 N284 T285 S305 G306 V333 G334 G335 L355 Y356 T357	A64 G65 S88 N113 N149 N180 K223 N252 T253 S273 G274 V301 G302 G303 L323 Y324 T325
BS02	DOR	A	N145 Y147 G148 F149 S215 N217 N284 T285	N113 Y115 G116 F117 S183 N185 N252 T253
BS03	6X1	A	M43 P52 H56 A59 F98 R136 Y356 L359 T360	M11 P20 H24 A27 F66 R104 Y324 L327 T328	MOAD: ic50=0.7uM BindingDB: IC50=700nM

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:3kvk, PDBe:3kvk, PDBj:3kvk
PDBsum	3kvk
PubMed	20153645
UniProt	Q02127\|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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