Structure of PDB 5dbf Chain B Binding Site BS01

Receptor Information
>5dbf Chain B (length=360) Species: 4058 (Catharanthus roseus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKK
PVEYIQCDVSDNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNIL
NSVIPNASNLQHVCLQTGIKHYFGIFEEVPHDSPFTEDLPRLNVPNFYHD
LEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHEN
KALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVF
KWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLV
PTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDK
MRDYRFIPAS
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain5dbf Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dbf Structures of Iridoid Synthase from Cantharanthus roseus with Bound NAD(+) , NADPH, or NAD(+) /10-Oxogeranial: Reaction Mechanisms
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G36 T38 G39 I40 A65 R66 R67 C83 D84 V85 S108 W109 M121 Q142 T143 Y178 A202 V204 S211 M212 M213
Binding residue
(residue number reindexed from 1)		G10 T12 G13 I14 A39 R40 R41 C57 D58 V59 S82 W83 M95 Q116 T117 Y148 A172 V174 S181 M182 M183
Annotation score4
Enzymatic activity
Enzyme Commision number 1.3.1.122: (S)-8-oxocitronellyl enol synthase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0016099 monoterpenoid biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5dbf, PDBe:5dbf, PDBj:5dbf
PDBsum5dbf
PubMed26768532
UniProtK7WDL7|IRIS_CATRO (S)-8-oxocitronellyl enol synthase

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