Structure of PDB 5eb5 Chain A Binding Site BS02

Receptor Information
>5eb5 Chain A (length=509) Species: 3755 (Prunus dulcis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANTSAHDFSYLKFVYNATDTSSEGSYDYIVIGGGTSGCPLAATLSEKYKV
LLLERGTIATEYPNTLTADGFAYNLQQQDDGKTPVERFVSEDGIDNVRAR
ILGGTTIINAGVYARANISFYSQTGIEWDLDLVNKTYEWVEDAIVVKPNN
QSWQSVIGEGFLEAGILPDNGFSLDHEAGTRLTGSTFDNNGTRHAADELL
NKGDPNNLLVAVQASVEKILFSNLSAIGVIYTDSDGNSHQAFVRGNGEVI
VSAGTIGTPQLLLLSGVGPESYLSSLNITVVQPNPYVGQFVYDNPRNFIN
ILPPNPIEASVATVLGIRSDYYQVSLSSLPFSTPPFSLFPTTSYPLPNST
FAHIVSQVPGPLSHGSVTLNSSSDVRIAPNIKFNYYSNSTDLANCVSGMK
KLGDLLRTKALEPYKARDVLGIDGFNYLGVPLPDASFETFCLDNVASYWH
YHGGSLVGKVLDDSFRVMGIKALRVVDASTFPYEPNSHPQGFYLMLGRYV
GLQILQERS
Ligand information
Ligand ID010
InChIInChI=1S/C7H8O/c8-6-7-4-2-1-3-5-7/h1-5,8H,6H2
InChIKeyWVDDGKGOMKODPV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01
CACTVS 3.370		OCc1ccccc1
OpenEye OEToolkits 1.7.0c1ccc(cc1)CO
FormulaC7 H8 O
Namephenylmethanol
ChEMBLCHEMBL720
DrugBankDB06770
ZINCZINC000000895302
PDB chain5eb5 Chain A Residue 609 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5eb5 Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		H358 Y458 W459 H498
Binding residue
(residue number reindexed from 1)		H353 Y448 W449 H488
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V329 Q362 Y458 H460 S497 H498
Catalytic site (residue number reindexed from 1) V324 Q357 Y448 H450 S487 H488
Enzyme Commision number 4.1.2.10: (R)-mandelonitrile lyase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0016829 lyase activity
GO:0046593 mandelonitrile lyase activity
GO:0050660 flavin adenine dinucleotide binding

View graph for
Molecular Function
External links
PDB RCSB:5eb5, PDBe:5eb5, PDBj:5eb5
PDBsum5eb5
PubMed27067080
UniProtO24243|MDL1_PRUDU (R)-mandelonitrile lyase 1 (Gene Name=MDL1)

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