Structure of PDB 3wcl Chain A Binding Site BS01

Receptor Information
>3wcl Chain A (length=334) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDD
MTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNL
AEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSR
LFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEV
WSRYVKKLGDFALPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSV
FNFCAIPQVMAIATLAACYNNQQVFKGAVLIRLGQAVTLMMDATNMPAVK
AIIYQYMEEIYHRIPDSNPSSSKTRQIISTIRTQ
Ligand information
Ligand IDBH3
InChIInChI=1S/C20H40N2O6P2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-21-16-17-22(19-21)18-20(29(23,24)25)30(26,27)28/h16-17,19-20H,2-15,18H2,1H3,(H3-,23,24,25,26,27,28)
InChIKeyVYLDLVZXAPQHHS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCC[n+]1ccn(c1)CC(P(=O)(O)O)P(=O)(O)[O-]
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCC[n+]1ccn(c1)C[C@@H](P(=O)(O)O)P(=O)(O)[O-]
CACTVS 3.370CCCCCCCCCCCCCCC[n+]1ccn(C[C@@H]([P](O)(O)=O)[P](O)([O-])=O)c1
CACTVS 3.370CCCCCCCCCCCCCCC[n+]1ccn(C[CH]([P](O)(O)=O)[P](O)([O-])=O)c1
ACDLabs 12.01[O-]P(=O)(O)C(P(=O)(O)O)Cn1cc[n+](c1)CCCCCCCCCCCCCCC
FormulaC20 H40 N2 O6 P2
Namehydrogen [(1R)-2-(3-pentadecyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate
ChEMBLCHEMBL2338383
DrugBank
ZINC
PDB chain3wcl 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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PDB3wcl Squalene synthase as a target for Chagas disease therapeutics.
Resolution2.24 Å
Binding residue
(original residue number in PDB)		S51 R52 S53 Y73 R77 D80 V179 M207 L211
Binding residue
(residue number reindexed from 1)		S16 R17 S18 Y38 R42 D45 V144 M172 L176
Annotation score1
Binding affinityMOAD: ic50=0.26uM
PDBbind-CN: -logKd/Ki=6.59,IC50=0.26uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y171 R218 R228 F288
Catalytic site (residue number reindexed from 1) Y136 R183 R193 F253
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:3wcl, PDBe:3wcl, PDBj:3wcl
PDBsum3wcl
PubMed24789335
UniProtP37268|FDFT_HUMAN Squalene synthase (Gene Name=FDFT1)

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