Structure of PDB 3kvm Chain A

Receptor sequence

>3kvmA (length=366) Species: 9606 (Homo sapiens) [Search protein sequence]

ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAEL
RRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGL
IVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPI
IGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKE
QGFGGVTDAIGADHRR

3D structure

PDB

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

Chain

Resolution

2.0 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)	G89 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 S120 N145 N181 N212 K255 N284 T285 S305 G306 V333 G334 G335 L355 Y356 T357	A66 G67 S90 N115 N151 N182 K225 N254 T255 S275 G276 V303 G304 G305 L325 Y326 T327
BS02	DOR	A	N145 Y147 G148 F149 S215 N217 N284 T285	N115 Y117 G118 F119 S185 N187 N254 T255
BS03	951	A	Y38 M43 P52 H56 A59 R136 Y356 T360 P364	Y8 M13 P22 H26 A29 R106 Y326 T330 P334	MOAD: ic50=0.5uM

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

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