Structure of PDB 8f6n Chain D Binding Site BS07

Receptor Information
>8f6n Chain D (length=992) 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
FYTSKDFLPLVAKSSKAGMSPLPSIRGAVIVLGAGDTAFDCATSALRCGA
RRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRIVAV
QFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSPIKF
NRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKY
IQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAPTTS
SSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPGQSS
FLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMELSRK
AEASGADALELNLSSPHMGLACGQDPELVRNICRWVRQAVQIPFFAKLTP
NVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTY
GGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSGASV
LQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESHQKG
KPVPRIAELMGKKLPNFGPYLEQRKKIIAEEERKPFIPKKPIPAIKDVIG
KALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSGYQAIQFDPE
THLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGLP
Ligand information
Ligand IDTDR
InChIInChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
InChIKeyRWQNBRDOKXIBIV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341
OpenEye OEToolkits 1.5.0		CC1=CNC(=O)NC1=O
ACDLabs 10.04O=C1C(=CNC(=O)N1)C
FormulaC5 H6 N2 O2
NameTHYMINE
ChEMBLCHEMBL993
DrugBankDB03462
ZINCZINC000000157062
PDB chain8f6n Chain D Residue 1107 [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]
PDB8f6n Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		N609 N668 N736 T737
Binding residue
(residue number reindexed from 1)		N603 N662 N724 T725
Annotation score5
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:8f6n, PDBe:8f6n, PDBj:8f6n
PDBsum8f6n
PubMed36681231
UniProtQ28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)

[Back to BioLiP]