Structure of PDB 3gdp Chain B Binding Site BS01

Receptor Information
>3gdp Chain B (length=521) Species: 3755 (Prunus dulcis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYK
VLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRG
RVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPN
SQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADEL
LNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSK
GEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPR
NFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSSSYPL
PNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCV
SGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFC
RESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQG
FYLMLGRYVGIKILQERSASD
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 chain3gdp Chain B Residue 523 [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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PDB3gdp Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		G33 G35 T36 E55 R56 V98 G105 T106 N110 A111 V113 V217 A257 W458 H459 G487 H497 P498 Q499 Y502
Binding residue
(residue number reindexed from 1)		G33 G35 T36 E55 R56 V98 G105 T106 N110 A111 V113 V217 A257 W458 H459 G487 H497 P498 Q499 Y502
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C328 K361 Y457 H459 S496 H497
Catalytic site (residue number reindexed from 1) C328 K361 Y457 H459 S496 H497
Enzyme Commision number 4.1.2.10: (R)-mandelonitrile lyase.
Gene Ontology
Molecular Function
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
Biological Process
GO:0050898 nitrile metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3gdp, PDBe:3gdp, PDBj:3gdp
PDBsum3gdp
PubMed19256550
UniProtQ945K2|MDL2_PRUDU (R)-mandelonitrile lyase 2 (Gene Name=MDL2)

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