Structure of PDB 8f6n Chain A Binding Site BS04

Receptor Information
>8f6n Chain A (length=996) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFH
CEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFI
TSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSIN
IGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASIS
CASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDL
GVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQ
GFYTSKDFLPLVAKSSKGMCPLSIRGAVIVLGAGDTAFDCATSALRCGAR
RVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRIVAVQ
FVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSPIKFN
RWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKYI
QAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAPTTSS
SMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPGQSSF
LNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMELSRKA
EASGADALELNLSSPHGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTP
NVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTY
GGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSGASV
LQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESHQKG
KPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKERKPFIPKKPIPAI
KDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSGYQAI
QFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGL
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain8f6n Chain A Residue 1104 [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)		C963 I971 C986 G988 C989 T990 C992
Binding residue
(residue number reindexed from 1)		C942 I950 C965 G967 C968 T969 C971
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:8f6n, PDBe:8f6n, PDBj:8f6n
PDBsum8f6n
PubMed36681231
UniProtQ28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)

[Back to BioLiP]