Structure of PDB 1yq4 Chain A Binding Site BS02

Receptor Information
>1yq4 Chain A (length=614) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISTQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHT
VAAQGGINAALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAV
IELENYGMPFSRTEEGKIYQRAFGGQSLQFGKGGQAHRCCCVADRTGHSL
LHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGTIHRFRAK
NTVIATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGI
YGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIE
IREGRGCGPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPI
PVLPTVHYNMGGIPTNYKGQVITHVNGEDKVVPGLYACGEAASASVHGAN
RLGANSLLDLVVFGRACALTIAETCKPGEPVPSIKPNAGEESVANLDKLR
FADGTIRTSEARLNMQKTMQSHAAVFRTGSILQEGCEKLSQIYRDLAHLK
TFDRGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKLR
IDEFDYSKPLQGQQKRPFEEHWRKHTLSYVDVKSGKVTLKYRPVIDRTLN
EEDCSSVPPAIRSY
Ligand information
Ligand ID3NP
InChIInChI=1S/C3H5NO4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)
InChIKeyWBLZUCOIBUDNBV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C[N+](=O)[O-])C(=O)O
ACDLabs 10.04[O-][N+](=O)CCC(=O)O
CACTVS 3.341OC(=O)CC[N+]([O-])=O
FormulaC3 H5 N O4
Name3-NITROPROPANOIC ACID
ChEMBLCHEMBL451226
DrugBank
ZINCZINC000000895862
PDB chain1yq4 Chain A Residue 1002 [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]
PDB1yq4 3-Nitropropionic Acid Is a Suicide Inhibitor of Mitochondrial Respiration That, upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme
Resolution2.33 Å
Binding residue
(original residue number in PDB)		G62 F130 H253 T265 E266 R297 H364
Binding residue
(residue number reindexed from 1)		G55 F123 H246 T258 E259 R290 H357
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) F130 Q251 H253 L263 E266 R269 R297 H364 Y365 R408
Catalytic site (residue number reindexed from 1) F123 Q244 H246 L256 E259 R262 R290 H357 Y358 R401
Enzyme Commision number 1.3.5.1: succinate dehydrogenase.
Gene Ontology
Molecular Function
GO:0008177 succinate dehydrogenase (quinone) activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0006105 succinate metabolic process
GO:0006121 mitochondrial electron transport, succinate to ubiquinone
GO:0022900 electron transport chain
GO:0022904 respiratory electron transport chain
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0045273 respiratory chain complex II (succinate dehydrogenase)

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1yq4, PDBe:1yq4, PDBj:1yq4
PDBsum1yq4
PubMed16371358
UniProtQ9YHT1|SDHA_CHICK Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (Gene Name=SDHA)

[Back to BioLiP]