Structure of PDB 5l1o Chain A Binding Site BS01

Receptor Information
>5l1o Chain A (length=397) Species: 29301 (Streptomyces arenae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDLPRLPFDNPDIMGIAPQMLALQKEGPIARVGTAGEDAWLVTRYDEVRT
LLADRRLRLSNPNPQPSAKSAARAFMVALMAGDDHETEPARHAQMRSLLI
PRFSTRRLRLMKTRIEHHVDELLDQLAASAPPVDLHRVLSFRLPTMVVCD
LLGVPLADRERFGQWARGTFDQSDNEHSANTFQQVVDYMLELVARKRVEP
GDDILSELIAEKDGALSDADIAHLGNAVLLFGYETTIVRIDLGTLLLLRN
PVQRAQLAEDPGLAPAAVEEILRLGVGGKGSNALIPRYAHGDITVGETVI
RTGDAVMLAIGAANYDDRAFPDGGLFDLTRVRPRSHLAFGHGARHCIGRT
LARIELTAVFERLFRRLPDLRLAVPEESLRWQEHRITGGFDEIPVTF
Ligand information
Ligand ID7PF
InChIInChI=1S/C15H18O5/c1-13(2)4-8-3-9(11(16)17)10-5-19-12(18)15(7-20-15)14(8,10)6-13/h3,8,10H,4-7H2,1-2H3,(H,16,17)/t8-,10+,14-,15-/m1/s1
InChIKeyUUDKOVSZNMZKND-BDAURDKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CC1(C[C@H]2C=C([C@H]3[C@]2(C1)[C@@]4(CO4)C(=O)OC3)C(=O)O)C
OpenEye OEToolkits 2.0.5CC1(CC2C=C(C3C2(C1)C4(CO4)C(=O)OC3)C(=O)O)C
CACTVS 3.385CC1(C)C[C@H]2C=C([C@@H]3COC(=O)[C@]4(CO4)[C@]23C1)C(O)=O
CACTVS 3.385CC1(C)C[CH]2C=C([CH]3COC(=O)[C]4(CO4)[C]23C1)C(O)=O
ACDLabs 12.01C2C3C=C(C(O)=O)C4COC(C1(CO1)C34CC2(C)C)=O
FormulaC15 H18 O5
Namepentalenolactone F;
(2R,4a'R,7a'S,9a'R)-6',6'-dimethyl-3'-oxo-1',5',6',7',7a',9a'-hexahydro-3'H-spiro[oxirane-2,4'-pentaleno[1,6a-c]pyran]-9'-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000034827642
PDB chain5l1o Chain A Residue 401 [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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PDB5l1o The Cytochrome P450-Catalyzed Oxidative Rearrangement in the Final Step of Pentalenolactone Biosynthesis: Substrate Structure Determines Mechanism.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		R74 F232 R240 N283 I387 T388
Binding residue
(residue number reindexed from 1)		R73 F231 R239 N282 I386 T387
Annotation score5
Binding affinityMOAD: Kd=7.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) D172 F232 E235 T236 T237 S282 C347 I348 G349 E356 T388
Catalytic site (residue number reindexed from 1) D171 F231 E234 T235 T236 S281 C346 I347 G348 E355 T387
Enzyme Commision number 1.14.19.8: pentalenolactone synthase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0016636 oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0017000 antibiotic biosynthetic process
GO:1901780 pentalenolactone biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5l1o, PDBe:5l1o, PDBj:5l1o
PDBsum5l1o
PubMed27588339
UniProtE3VWI3|PNTM_STRAE Pentalenolactone synthase (Gene Name=pntM)

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