Structure of PDB 8f61 Chain B Binding Site BS06

Receptor Information
>8f61 Chain B (length=1016) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHC
EKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFIT
SISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINI
GGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISC
ASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLG
VKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQG
FYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSAL
RCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGR
IVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALS
PIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWY
IHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAA
PTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGP
GQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWME
LSRKAEASGADALELNLSSPHGMGERGMGLACGQDPELVRNICRWVRQAV
QIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWP
AVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESG
LQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQ
SPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNA
AFPPLERKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEM
CINCGKCYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCI
RMVSRTTPYEPKRGLP
Ligand information
Ligand IDFMN
InChIInChI=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
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain8f61 Chain B Residue 1106 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8f61 Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
Resolution2.14 Å
Binding residue
(original residue number in PDB)		S550 A551 K574 T575 N609 N668 K709 N736 S766 G767 T793 G794 G795 C816 S817
Binding residue
(residue number reindexed from 1)		S548 A549 K572 T573 N607 N666 K707 N734 S764 G765 T791 G792 G793 C814 S815
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.1.2: dihydropyrimidine dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002058 uracil binding
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0050661 NADP binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006210 thymine catabolic process
GO:0006212 uracil catabolic process
GO:0006214 thymidine catabolic process
GO:0019483 beta-alanine biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8f61, PDBe:8f61, PDBj:8f61
PDBsum8f61
PubMed36681231
UniProtQ28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)

[Back to BioLiP]