Structure of PDB 6fmd Chain A Binding Site BS02

Receptor Information

>6fmd Chain A (length=357) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPGKAELRRLLTKVLQ
ERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSR
PAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSG
QDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDA
IGADHRR

Ligand information

Ligand ID

FMN

InChI

InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1

InChIKey

FVTCRASFADXXNN-SCRDCRAPSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6	Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01	N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385	Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385	Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C

Formula

C17 H21 N4 O9 P

Name

FLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE

PDB chain

6fmd Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6fmd Targeting Myeloid Differentiation Using Potent 2-Hydroxypyrazolo[1,5- a]pyridine Scaffold-Based Human Dihydroorotate Dehydrogenase Inhibitors.
Resolution	1.58 Å
Binding residue (original residue number in PDB)	A96 G97 K100 S120 N145 N181 N212 K255 N284 T285 S305 G306 G334 G335 Y356 T357
Binding residue (residue number reindexed from 1)	A66 G67 K70 S90 N115 N151 N182 K216 N245 T246 S266 G267 G295 G296 Y317 T318
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	G119 N145 F149 S215 K255 N284
Catalytic site (residue number reindexed from 1)	G89 N115 F119 S185 K216 N245
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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Cellular Component

External links

PDB	RCSB:6fmd, PDBe:6fmd, PDBj:6fmd
PDBsum	6fmd
PubMed	29939742
UniProt	Q02127\|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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