Structure of PDB 2vzm Chain A Binding Site BS02

Receptor Information
>2vzm Chain A (length=395) Species: 54571 (Streptomyces venezuelae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRA
RAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREF
TMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELL
GVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGE
DLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLS
HPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPA
GDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLAR
LEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR
Ligand information
Ligand IDNRB
InChIInChI=1S/C28H47NO7/c1-10-23-15(2)11-12-22(30)16(3)13-17(4)26(19(6)24(31)20(7)27(33)35-23)36-28-25(32)21(29(8)9)14-18(5)34-28/h11-12,15-21,23,25-26,28,32H,10,13-14H2,1-9H3/b12-11+/t15-,16-,17+,18+,19-,20-,21-,23-,25-,26+,28-/m1/s1
InChIKeyOXFYAOOMMKGGAI-ZMIJTAGNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC[CH]1OC(=O)[CH](C)C(=O)[CH](C)[CH](O[CH]2O[CH](C)C[CH]([CH]2O)N(C)C)[CH](C)C[CH](C)C(=O)C=C[CH]1C
OpenEye OEToolkits 1.5.0CCC1C(C=CC(=O)C(CC(C(C(C(=O)C(C(=O)O1)C)C)OC2C(C(CC(O2)C)N(C)C)O)C)C)C
OpenEye OEToolkits 1.5.0CC[C@@H]1[C@@H](\C=C\C(=O)[C@@H](C[C@@H]([C@@H]([C@@H](C(=O)[C@H](C(=O)O1)C)C)O[C@@H]2[C@@H]([C@@H](C[C@@H](O2)C)N(C)C)O)C)C)C
CACTVS 3.341CC[C@H]1OC(=O)[C@H](C)C(=O)[C@@H](C)[C@@H](O[C@H]2O[C@@H](C)C[C@H]([C@H]2O)N(C)C)[C@@H](C)C[C@@H](C)C(=O)\C=C\[C@H]1C
ACDLabs 10.04O=C2C(C(OC1OC(CC(N(C)C)C1O)C)C(C)CC(C(=O)C=CC(C)C(OC(=O)C2C)CC)C)C
FormulaC28 H47 N O7
NameNARBOMYCIN
ChEMBL
DrugBank
ZINCZINC000016051866
PDB chain2vzm Chain A Residue 1408 [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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PDB2vzm Analysis of Transient and Catalytic Desosamine Binding Pockets in Cytochrome P450 Pikc from Streptomyces Venezuelae.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		F178 M191 I239 T247 I395
Binding residue
(residue number reindexed from 1)		F167 M180 I228 T236 I384
Annotation score5
Binding affinityMOAD: Kd=171.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) D23 P47 F180 A243 E246 T247 T248 V290 C354 I355 G356 E363 I395
Catalytic site (residue number reindexed from 1) D12 P36 F169 A232 E235 T236 T237 V279 C343 I344 G345 E352 I384
Enzyme Commision number 1.14.15.33: pikromycin synthase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
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:0033068 macrolide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vzm, PDBe:2vzm, PDBj:2vzm
PDBsum2vzm
PubMed19124459
UniProtO87605|PIKC_STRVZ Cytochrome P450 monooxygenase PikC (Gene Name=pikC)

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