Structure of PDB 6lqy Chain A Binding Site BS01

Receptor Information
>6lqy Chain A (length=517) Species: 3755 (Prunus dulcis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHLANTSAHDFSYLKFVYNATDTSLEGSYDYIVIGGGTSGCPLAATLS
EKYKVLLLERGTIATEYPNTLTADGFAYNLQQQDDGKTPVERFVSEDGID
NVRARILGGTTIINAGVYARANISFYSQTGIEWDLDLVNKTYEWVEDAIV
VKPNNQSWQSVIGEGFLEAGILPDNGFSLDHEAGTRLTGSTFDNNGTRHA
ADELLNKGDPNNLLVAVQASVEKILFSSNLSAIGVIYTDSDGNSHQAFVR
GNGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNITVVQPNPYVGQFVYDN
PRNFINILPPNPIEASVVTVLGIRSDYYQVSLSSLPFSTPPFSLFPTTSY
PLPNSTFAHIVSQVPGPLSHGSVTLNSSSDVRIAPNIKFNYYSNSTDLAN
CVSGMKKLGDLLRTKALEPYKARDVLGIDGFNYLGVPLPTDDASFETFCL
DNVASYWHYHGGSLVGKVLDDSFRVMGIKALRVVDASTFPYEPNSHPQGF
YLMLGRYVGLQILQERS
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 chain6lqy 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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PDB6lqy Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.
Resolution1.598 Å
Binding residue
(original residue number in PDB)		G33 T36 E55 R56 A100 G105 T106 N110 A111 V113 V217 A258 W459 H460 A488 H498 P499 Q500
Binding residue
(residue number reindexed from 1)		G37 T40 E59 R60 A104 G109 T110 N114 A115 V117 V221 A259 W457 H458 A486 H496 P497 Q498
Annotation score1
Enzymatic activity
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:6lqy, PDBe:6lqy, PDBj:6lqy
PDBsum6lqy
PubMed
UniProtO24243|MDL1_PRUDU (R)-mandelonitrile lyase 1 (Gene Name=MDL1)

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