Structure of PDB 3vje Chain A Binding Site BS01

Receptor Information
>3vje Chain A (length=284) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTMMDMNFKYCHKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDS
IDVYGDIQFLNQIKEDIQSIEKYPYEYHHFQSDRRIMMALQHVAQHKNIA
FQSFYNLIDTVYKDQHFTMFETDAELFGYCYGVAGTVGEVLTPILSDHET
HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEVY
QNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFSIEAQPIIELAARIAIE
ILDEVRQANYTLHERVFVEKRKKAKLFHEINSKY
Ligand information
Ligand IDZGA
InChIInChI=1S/C35H46O14/c1-7-19(2)17-20(3)13-14-25(37)47-28-27(38)33(48-29(30(39)40)34(45,31(41)42)35(28,49-33)32(43)44)16-15-21(4)26(46-23(6)36)22(5)18-24-11-9-8-10-12-24/h8-14,19-20,22,26-29,38,45H,4,7,15-18H2,1-3,5-6H3,(H,39,40)(H,41,42)(H,43,44)/b14-13+/t19-,20+,22+,26+,27+,28+,29+,33-,34+,35-/m0/s1
InChIKeyDFKDOZMCHOGOBR-NCSQYGPNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC[C@H](C)C[C@H](C)/C=C/C(=O)O[C@@H]1[C@H]([C@]2(O[C@@H]([C@]([C@@]1(O2)C(=O)O)(C(=O)O)O)C(=O)O)CCC(=C)[C@H]([C@H](C)Cc3ccccc3)OC(=O)C)O
CACTVS 3.370CC[C@H](C)C[C@H](C)/C=C/C(=O)O[C@@H]1[C@@H](O)[C@@]2(CCC(=C)[C@@H](OC(C)=O)[C@H](C)Cc3ccccc3)O[C@H](C(O)=O)[C@@](O)(C(O)=O)[C@@]1(O2)C(O)=O
CACTVS 3.370CC[CH](C)C[CH](C)C=CC(=O)O[CH]1[CH](O)[C]2(CCC(=C)[CH](OC(C)=O)[CH](C)Cc3ccccc3)O[CH](C(O)=O)[C](O)(C(O)=O)[C]1(O2)C(O)=O
OpenEye OEToolkits 1.7.2CCC(C)CC(C)C=CC(=O)OC1C(C2(OC(C(C1(O2)C(=O)O)(C(=O)O)O)C(=O)O)CCC(=C)C(C(C)Cc3ccccc3)OC(=O)C)O
ACDLabs 12.01O=C(O)C1(O)C(OC2(OC1(C(=O)O)C(OC(=O)/C=C/C(C)CC(C)CC)C2O)CCC(=C)\C(OC(=O)C)C(C)Cc3ccccc3)C(=O)O
FormulaC35 H46 O14
NameZaragozic acid A;
(1S,3S,4S,5R,6R,7R)-1-[(4S,5R)-4-(acetyloxy)-5-methyl-3-methylidene-6-phenylhexyl]-6-{[(2E,4S,6S)-4,6-dimethyloct-2-eno yl]oxy}-4,7-dihydroxy-2,8-dioxabicyclo[3.2.1]octane-3,4,5-tricarboxylic acid
ChEMBLCHEMBL280978
DrugBank
ZINCZINC000034803452
PDB chain3vje Chain A Residue 301 [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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PDB3vje Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase
Resolution2.12 Å
Binding residue
(original residue number in PDB)		H18 S19 K20 S21 F22 F26 Y41 C44 R45 D48 L107 V137 L164 N168 R171 A244 R265
Binding residue
(residue number reindexed from 1)		H18 S19 K20 S21 F22 F26 Y41 C44 R45 D48 L107 V137 L164 N168 R171 A244 R265
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.01,Kd=9.7nM
Enzymatic activity
Enzyme Commision number 2.5.1.96: 4,4'-diapophytoene synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004311 farnesyltranstransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0016767 geranylgeranyl-diphosphate geranylgeranyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process
GO:0016117 carotenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vje, PDBe:3vje, PDBj:3vje
PDBsum3vje
PubMed22474324
UniProtA9JQL9|CRTM_STAAU 4,4'-diapophytoene synthase (Gene Name=crtM)

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