Structure of PDB 1gt8 Chain D Binding Site BS08

Receptor Information
>1gt8 Chain D (length=1012) 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
GFYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSA
LRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGG
RIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEAL
SPIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASW
YIHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASA
APTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYG
PGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM
ELSRKAEASGADALELNLSCPHGMGMGLACGQDPELVRNICRWVRQAVQI
PFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAV
GAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQ
FLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSP
GTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNPLE
RKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGK
CYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRT
TPYEPKRGLPLA
Ligand information
Ligand IDUAA
InChIInChI=1S/C6H6N2O4/c9-4-1-3(2-5(10)11)7-6(12)8-4/h1H,2H2,(H,10,11)(H2,7,8,9,12)
InChIKeyNQAUNZZEYKWTHM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=CC(=O)N1)CC(=O)O
CACTVS 3.341OC(=O)CC1=CC(=O)NC(=O)N1
OpenEye OEToolkits 1.5.0C1=C(NC(=O)NC1=O)CC(=O)O
FormulaC6 H6 N2 O4
NameURACIL-6-ACETIC ACID;
6-CARBOXYMETHYLURACIL
ChEMBLCHEMBL593503
DrugBankDB03048
ZINCZINC000000403617
PDB chain1gt8 Chain D Residue 1035 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1gt8 Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		N609 E611 I613 T737
Binding residue
(residue number reindexed from 1)		N608 E610 I612 T733
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K574 G601 S605 C671 H673 G674 K709 T735
Catalytic site (residue number reindexed from 1) K573 G600 S604 C670 H672 G673 K705 T731
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1gt8, PDBe:1gt8, PDBj:1gt8
PDBsum1gt8
PubMed11796730
UniProtQ28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)

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