Structure of PDB 2yd0 Chain A Binding Site BS02

Receptor Information
>2yd0 Chain A (length=858) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFPWNKIRLPEYVIPVHYDLLIHANLTTLTFWGTTKVEITASQPTSTIIL
HSHHLQISRATLRKGLSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVI
HYAGNLSETFHGFYKSTYRTKEGELRILASTQFEPTAARMAFPCFDEPAF
KASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAF
IISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVTLLEFYEDYFSI
PYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLGITM
TVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDY
FFGKCFDAMEVDALNSSHPVSTPVENPAQIREMFDDVSYDKGACILNMLR
EYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASIGVDVKTMMNTWTLQ
KGFPLITITVRGRNVHMKQEHYMKGDTGYLWHVPLTFITSKSDMVHRFLL
KTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVS
SNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNELIP
MYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSQLL
LLACVHNYQPCVQRAEGYFRKWKESNGNLSLPVDVTLAVFAVGAQSTEGW
DFLYSKYQFSLSSTEKSQIEFALCRTQNKEKLQWLLDESFKGDKIKTQEF
PQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTTNQF
STRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNFDKIRVW
LQSEKLER
Ligand information
Ligand IDBES
InChIInChI=1S/C16H24N2O4/c1-10(2)8-13(16(21)22)18-15(20)14(19)12(17)9-11-6-4-3-5-7-11/h3-7,10,12-14,19H,8-9,17H2,1-2H3,(H,18,20)(H,21,22)/t12-,13+,14+/m1/s1
InChIKeyVGGGPCQERPFHOB-RDBSUJKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C[C@@H](C(=O)O)NC(=O)[C@H]([C@@H](Cc1ccccc1)N)O
CACTVS 3.341CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C(O)=O
ACDLabs 10.04O=C(O)C(NC(=O)C(O)C(N)Cc1ccccc1)CC(C)C
OpenEye OEToolkits 1.5.0CC(C)CC(C(=O)O)NC(=O)C(C(Cc1ccccc1)N)O
CACTVS 3.341CC(C)C[CH](NC(=O)[CH](O)[CH](N)Cc1ccccc1)C(O)=O
FormulaC16 H24 N2 O4
Name2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID;
BESTATIN
ChEMBLCHEMBL29292
DrugBankDB03424
ZINCZINC000001542895
PDB chain2yd0 Chain A Residue 1950 [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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PDB2yd0 Crystal Structures of the Endoplasmic Reticulum Aminopeptidase-1 (Erap1) Reveal the Molecular Basis for N-Terminal Peptide Trimming.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Q181 E183 S316 G317 A318 M319 E320 H353 E354 H357 E376 K380 Y438
Binding residue
(residue number reindexed from 1)		Q132 E134 S267 G268 A269 M270 E271 H304 E305 H308 E327 K331 Y389
Annotation score3
Binding affinityBindingDB: IC50=50000nM
Enzymatic activity
Catalytic site (original residue number in PDB) E320 H353 E354 H357 E376 R430 Y438
Catalytic site (residue number reindexed from 1) E271 H304 E305 H308 E327 R381 Y389
Enzyme Commision number 3.4.11.-
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004177 aminopeptidase activity
GO:0005138 interleukin-6 receptor binding
GO:0005151 interleukin-1, type II receptor binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008235 metalloexopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0042277 peptide binding
GO:0046872 metal ion binding
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0001525 angiogenesis
GO:0002250 adaptive immune response
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0006508 proteolysis
GO:0006509 membrane protein ectodomain proteolysis
GO:0008217 regulation of blood pressure
GO:0009617 response to bacterium
GO:0019885 antigen processing and presentation of endogenous peptide antigen via MHC class I
GO:0043171 peptide catabolic process
GO:0045088 regulation of innate immune response
GO:0045444 fat cell differentiation
GO:0045766 positive regulation of angiogenesis
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yd0, PDBe:2yd0, PDBj:2yd0
PDBsum2yd0
PubMed21508329
UniProtQ9NZ08|ERAP1_HUMAN Endoplasmic reticulum aminopeptidase 1 (Gene Name=ERAP1)

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