Structure of PDB 6v3h Chain A Binding Site BS02

Receptor Information
>6v3h Chain A (length=1232) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYTPKHEAGVCTFYEECGKNPELSGGLTSLSNVSCLSNTPARHVTGEHLA
LLQRICPRLYNGPNTTFACCSTKQLLSLESSMSITKALLTRCPACSDNFV
SLHCHNTCSPDQSLFINVTRVVERGAGEPPAVVAYEAFYQRSFAEKAYES
CSQVRIPAAASLAVGSMCGVYGSALCNAQRWLNFQGDTGNGLAPLDITFH
LLEPGQALPDGIQPLNGKIAPCNESQGDDSAVCSCQDCAASCPVIPPPEA
LRPSFYMGRMPGWLALIIIFTAVFVLLSAVLVRLRVVSNRNKSPHTILGR
FFQNWGTRVASWPLTVLALSFIVVIALAAGLTFIELTTDPVELWSAPKSQ
ARKEKSFHDEHFGPFFRTNQIFVTARNRSSYKYDSLLLGSKNFSGILSLD
FLLELLELQERLRHLQVWSPEAERNISLQDICYAPLNPYNTSLSDCCVNS
LLQYFQNNRTLLMLTANQTLNGQTSLVDWKDHFLYCANAPLTFKDGTSLA
LSCMADYGAPVFPFLAVGGYQGTDYSEAEALIITFSLNNYPADDPRMAQA
KLWEEAFLKEMESFQRNTSDKFQVAFSAERSLEDEINRTTIQDLPVFAVS
YIIVFLYISLALGSYSRCSRVAVESKATLGLGGVIVVLGAVLAAMGFYSY
LGVPSSLVIIQVVPFLVLAVGADNIFIFVLEYQRLPRMPGEQREAHIGRT
LGSVAPSMLLCSLSEAICFFLGALTPMPAVRTFALTSGLAIILDFLLQMT
AFVALLSLDSKRQEASRPDVLCCKEGLLLRFFRKIYAPFLLHRFIRPVVM
LLFLTLFGANLYLMCNINVGLDQELALPKDSYLIDYFLFLNRYLEVGPPV
YFVTTSGFNFSSEAGMNATCSSAGCKSFSLTQKIQYASEFPDQSYVAIAA
SSWVDDFIDWLTPSSSCCRLYIRGPHKDEFCPSTDTSFNCLKNCMNRTLG
PVRPTAEQFHKYLPWFLNDPPNIRCPKGGLAAYRTSVNLSSDGQVIASQF
MAYHKPLRNSQDFTEALRASRLLAANITADLRKVPGTDPNFEVFPYTISN
VFYQQYLTVLPEGIFTLALCFVPTFVVCYLLLGLDMCSGILNLLSIIMIL
VDTIGLMAVWGISYNAVSLINLVTAVGMSVEFVSHITRSFAVSTKPTRLE
RAKDATVFMGSAVFAGVAMTNFPGILILGFAQAQLIQIFFFRLNLLITLL
GLLHGLVFLPVVLSYLGPDVNQALVQEEKLAS
Ligand information
Ligand IDQO1
InChIInChI=1S/C34H35FN2O11S/c1-49(45,46)36-18-2-3-19-4-12-23(13-5-19)37-27(25(32(37)42)16-17-26(38)20-6-10-22(35)11-7-20)21-8-14-24(15-9-21)47-34-30(41)28(39)29(40)31(48-34)33(43)44/h4-15,25-31,34,36,38-41H,16-18H2,1H3,(H,43,44)/t25-,26+,27-,28+,29+,30-,31+,34-/m1/s1
InChIKeyDWURZHBEXYXPMW-WHTAKPIKSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1(ccc(cc1)C(CCC4C(c2ccc(cc2)OC3C(C(C(C(C(=O)O)O3)O)O)O)N(C4=O)c5ccc(cc5)C#CCNS(C)(=O)=O)O)F
CACTVS 3.385C[S](=O)(=O)NCC#Cc1ccc(cc1)N2[C@@H]([C@@H](CC[C@H](O)c3ccc(F)cc3)C2=O)c4ccc(O[C@@H]5O[C@@H]([C@@H](O)[C@H](O)[C@H]5O)C(O)=O)cc4
CACTVS 3.385C[S](=O)(=O)NCC#Cc1ccc(cc1)N2[CH]([CH](CC[CH](O)c3ccc(F)cc3)C2=O)c4ccc(O[CH]5O[CH]([CH](O)[CH](O)[CH]5O)C(O)=O)cc4
OpenEye OEToolkits 2.0.7CS(=O)(=O)NCC#Cc1ccc(cc1)N2C(C(C2=O)CCC(c3ccc(cc3)F)O)c4ccc(cc4)OC5C(C(C(C(O5)C(=O)O)O)O)O
OpenEye OEToolkits 2.0.7CS(=O)(=O)NCC#Cc1ccc(cc1)N2[C@@H](C(C2=O)CC[C@@H](c3ccc(cc3)F)O)c4ccc(cc4)O[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)C(=O)O)O)O)O
FormulaC34 H35 F N2 O11 S
Name4-[(2S,3R)-3-[(3S)-3-(4-fluorophenyl)-3-hydroxypropyl]-1-(4-{3-[(methylsulfonyl)amino]prop-1-yn-1-yl}phenyl)-4-oxoazetidin-2-yl]phenyl beta-D-glucopyranosiduronic acid
ChEMBLCHEMBL1908941
DrugBank
ZINCZINC000049722543
PDB chain6v3h Chain A Residue 1421 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6v3h Cryo-EM structures of NPC1L1 reveal mechanisms of cholesterol transport and ezetimibe inhibition
Resolution3.5 Å
Binding residue
(original residue number in PDB)		S187 L213 P474 L475 L530 F532 G547 A548 P1021 N1022 A1031
Binding residue
(residue number reindexed from 1)		S166 L192 P435 L436 L491 F493 G508 A509 P971 N972 A981
Annotation score1
Binding affinityBindingDB: IC50=4nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005319 lipid transporter activity
GO:0008431 vitamin E binding
GO:0015485 cholesterol binding
GO:0031267 small GTPase binding
GO:0031489 myosin V binding
GO:0042803 protein homodimerization activity
GO:1901363 heterocyclic compound binding
Biological Process
GO:0006695 cholesterol biosynthetic process
GO:0008203 cholesterol metabolic process
GO:0009410 response to xenobiotic stimulus
GO:0014850 response to muscle activity
GO:0030299 intestinal cholesterol absorption
GO:0030301 cholesterol transport
GO:0042157 lipoprotein metabolic process
GO:0042360 vitamin E metabolic process
GO:0042632 cholesterol homeostasis
GO:0051180 vitamin transport
GO:0070508 cholesterol import
GO:0071501 cellular response to sterol depletion
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0031526 brush border membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6v3h, PDBe:6v3h, PDBj:6v3h
PDBsum6v3h
PubMed
UniProtQ6T3U3|NPCL1_RAT NPC1-like intracellular cholesterol transporter 1 (Gene Name=Npc1l1)

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