Structure of PDB 4y6k Chain D Binding Site BS01

Receptor Information
>4y6k Chain D (length=237) Species: 368407 (Methanoculleus marisnigri JR1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WLPLLGMPLMLLFVQIIAIVLVMPMQAPSSVANPLIFIGMLLAFTLVLLV
LLRTGGRRFIAAFIGFALFMTFLYIFGALSLLALGPTTAAAAGTLIGAVA
VTALLYLYPEWYVIDILGVLISAGVASIFGISLEPLPVLVLLVLLAVYDA
ISVYRTKHMITLAEGVGAFVMGMGDLIMPSILVVSSHVFVSAPTLGAMVG
SLVGLAVLLYFVNKGNPQAGLPPLNGGAILGFLVGAA
Ligand information
Ligand ID4B5
InChIInChI=1S/C39H52N4O6/c1-26(2)21-33(37(47)41-32(35(40)45)24-29-19-13-8-14-20-29)42-36(46)30(22-27-15-9-6-10-16-27)25-34(44)31(23-28-17-11-7-12-18-28)43-38(48)49-39(3,4)5/h6-20,26,30-34,44H,21-25H2,1-5H3,(H2,40,45)(H,41,47)(H,42,46)(H,43,48)/t30-,31+,32+,33+,34+/m1/s1
InChIKeyMURCDOXDAHPNRQ-OWIQAHIBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(C)CC(C(=O)NC(Cc1ccccc1)C(=O)N)NC(=O)C(Cc2ccccc2)CC(C(Cc3ccccc3)NC(=O)OC(C)(C)C)O
OpenEye OEToolkits 1.9.2CC(C)C[C@@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)N)NC(=O)[C@H](Cc2ccccc2)C[C@@H]([C@H](Cc3ccccc3)NC(=O)OC(C)(C)C)O
CACTVS 3.385CC(C)C[C@H](NC(=O)[C@@H](C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C)Cc2ccccc2)C(=O)N[C@@H](Cc3ccccc3)C(N)=O
CACTVS 3.385CC(C)C[CH](NC(=O)[CH](C[CH](O)[CH](Cc1ccccc1)NC(=O)OC(C)(C)C)Cc2ccccc2)C(=O)N[CH](Cc3ccccc3)C(N)=O
ACDLabs 12.01O=C(N)C(NC(=O)C(NC(=O)C(Cc1ccccc1)CC(O)C(NC(=O)OC(C)(C)C)Cc2ccccc2)CC(C)C)Cc3ccccc3
FormulaC39 H52 N4 O6
NameN-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide
ChEMBLCHEMBL289195
DrugBank
ZINCZINC000003933965
PDB chain4y6k Chain D Residue 501 [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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PDB4y6k Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH
Resolution3.855 Å
Binding residue
(original residue number in PDB)		L158 A159 Y161 D162 V215 M216 M223 L275 N279
Binding residue
(residue number reindexed from 1)		L145 A146 Y148 D149 V170 M171 M178 L221 N225
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042500 aspartic endopeptidase activity, intramembrane cleaving
GO:0042802 identical protein binding
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:4y6k, PDBe:4y6k, PDBj:4y6k
PDBsum4y6k
PubMed25733893
UniProtA3CWV0

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