Structure of PDB 8f5w Chain B Binding Site BS02

Receptor Information
>8f5w Chain B (length=1012) 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
LSRKAEASGADALELNLSSPHGLACGQDPELVRNICRWVRQAVQIPFFAK
LTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKR
TTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSG
ASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESH
QKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNAAFPPLER
KPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKC
YMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTT
PYEPKRGLPLAV
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 chain8f5w Chain B Residue 1102 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8f5w Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		I948 C953 I954 N955 C956 G957 C959 P980 C996 P997 C1001 I1002
Binding residue
(residue number reindexed from 1)		I939 C944 I945 N946 C947 G948 C950 P971 C987 P988 C992 I993
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8f5w, PDBe:8f5w, PDBj:8f5w
PDBsum8f5w
PubMed36681231
UniProtQ28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)

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