Structure of PDB 6lr8 Chain A Binding Site BS01

Receptor Information
>6lr8 Chain A (length=518) Species: 3755 (Prunus dulcis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHHHLANTSAHDFSYLKFVYNATDTSLEGSYDYIVIGGGTSGCPLAAT
LSEKYKVLLLERGTIATEYPNTLTADGFAYNLQQQDDGKTPVERFVSEDG
IDNVRARILGGTTIINAGVYARANISFYSQTGIEWDLDLVNKTYEWVEDA
IVVKPNNQSWQSVIGEGFLEAGILPDNGFSLDHEAGTRLTGSTFDNNGTR
HAADELLNKGDPNNLLVAVQASVEKILFSSNLSAIGVIYTDSDGNSHQAF
VRGNGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNITVVQPNPYVGQFVY
DNPRNFINILPPNPIEASVVTVLGIRSDYYQVSASSLPFSTPPFSLFPTT
SYPLPNSTFAHIVSQVPGPLSHGSVTLNSSSDVRIAPNIKFNYYSNSTDL
ANCVSGMKKLGDLLRTKALEPYKARDVLGIDGFNYLGVPLPDDASFETFC
LDNVASYWHYHGGSLVGKVLDDSFRVMGIKALRVVDASTFPYEPNSHPQG
FYLMLGRYVGLQILQERS
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 chain6lr8 Chain A Residue 609 [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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PDB6lr8 Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.
Resolution1.595 Å
Binding residue
(original residue number in PDB)		G33 G35 T36 E55 R56 A100 G105 T106 N110 A111 V113 V217 A258 W459 H460 A488 H498 P499 Q500
Binding residue
(residue number reindexed from 1)		G39 G41 T42 E61 R62 A106 G111 T112 N116 A117 V119 V223 A261 W458 H459 A487 H497 P498 Q499
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:6lr8, PDBe:6lr8, PDBj:6lr8
PDBsum6lr8
PubMed
UniProtO24243|MDL1_PRUDU (R)-mandelonitrile lyase 1 (Gene Name=MDL1)

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