Structure of PDB 5eb4 Chain A Binding Site BS01

Receptor Information
>5eb4 Chain A (length=515) 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
NKGDPNNLLVAVQASVEKILFSSNLSAIGVIYTDSDGNSHQAFVRGNGEV
IVSAGTIGTPQLLLLSGVGPESYLSSLNITVVQPNPYVGQFVYDNPRNFI
NILPPNPIEASVATVLGIRSDYYQVSLSSLPFSTPPFSLFPTTSYPLPNS
TFAHIVSQVPGPLSHGSVTLNSSSDVRIAPNIKFNYYSNSTDLANCVSGM
KKLGDLLRTKALEPYKARDVLGIDGFNYLGVPLPENQTDDASFETFCLDN
VASYWHYHGGSLVGKVLDDSFRVMGIKALRVVDASTFPYEPNSHPQGFYL
MLGRYVGLQILQERS
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain5eb4 Chain A Residue 608 [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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PDB5eb4 Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G33 G35 T36 E55 R56 A100 T106 N110 A111 V113 V217 A258 W459 H460 A488 H498 P499 Q500
Binding residue
(residue number reindexed from 1)		G32 G34 T35 E54 R55 A99 T105 N109 A110 V112 V216 A254 W455 H456 A484 H494 P495 Q496
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V329 Q362 Y458 H460 S497 H498
Catalytic site (residue number reindexed from 1) V325 Q358 Y454 H456 S493 H494
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:5eb4, PDBe:5eb4, PDBj:5eb4
PDBsum5eb4
PubMed27067080
UniProtO24243|MDL1_PRUDU (R)-mandelonitrile lyase 1 (Gene Name=MDL1)

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