Structure of PDB 5eky Chain A Binding Site BS01

Receptor Information
>5eky Chain A (length=248) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRF
IPIARETLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAWGADEVD
VVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIR
KASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFKP
AGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGH
Ligand information
Ligand IDBU2
InChIInChI=1S/C4H10O2/c1-4(6)2-3-5/h4-6H,2-3H2,1H3/t4-/m0/s1
InChIKeyPUPZLCDOIYMWBV-BYPYZUCNSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04OCCC(O)C
OpenEye OEToolkits 1.5.0C[C@@H](CCO)O
CACTVS 3.341C[CH](O)CCO
CACTVS 3.341C[C@H](O)CCO
OpenEye OEToolkits 1.5.0CC(CCO)O
FormulaC4 H10 O2
Name1,3-BUTANEDIOL
ChEMBLCHEMBL1231501
DrugBankDB02202
ZINCZINC000001867144
PDB chain5eky Chain A Residue 301 [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]
PDB5eky Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies.
Resolution1.1 Å
Binding residue
(original residue number in PDB)		K167 T170 G171 A203 H250
Binding residue
(residue number reindexed from 1)		K165 T168 G169 A201 H248
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D102 K167 K201
Catalytic site (residue number reindexed from 1) D100 K165 K199
Enzyme Commision number 4.1.2.4: deoxyribose-phosphate aldolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004139 deoxyribose-phosphate aldolase activity
GO:0016829 lyase activity
Biological Process
GO:0006018 2-deoxyribose 1-phosphate catabolic process
GO:0006974 DNA damage response
GO:0009264 deoxyribonucleotide catabolic process
GO:0015949 nucleobase-containing small molecule interconversion
GO:0016052 carbohydrate catabolic process
GO:0046386 deoxyribose phosphate catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5eky, PDBe:5eky, PDBj:5eky
PDBsum5eky
PubMed30155096
UniProtP0A6L0|DEOC_ECOLI Deoxyribose-phosphate aldolase (Gene Name=deoC)

[Back to BioLiP]