Structure of PDB 3vjc Chain F Binding Site BS01

Receptor Information
>3vjc Chain F (length=332) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMT
ISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAE
KYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLF
SASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWS
RYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFN
FCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAI
IYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQ
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 chain3vjc Chain F Residue 400 [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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PDB3vjc Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase
Resolution1.89 Å
Binding residue
(original residue number in PDB)		T50 S51 R52 S53 F54 Y73 R77 D80 V179 L211 N215 F288 M295
Binding residue
(residue number reindexed from 1)		T13 S14 R15 S16 F17 Y36 R40 D43 V142 L174 N178 F251 M258
Annotation score1
Binding affinityBindingDB: IC50=5nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y171 R218 R228 F288
Catalytic site (residue number reindexed from 1) Y134 R181 R191 F251
Enzyme Commision number 2.5.1.21: squalene synthase.
Gene Ontology
Molecular Function
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0051996 squalene synthase [NAD(P)H] activity
Biological Process
GO:0008610 lipid biosynthetic process
GO:0009058 biosynthetic process
GO:0045338 farnesyl diphosphate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vjc, PDBe:3vjc, PDBj:3vjc
PDBsum3vjc
PubMed22474324
UniProtP37268|FDFT_HUMAN Squalene synthase (Gene Name=FDFT1)

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