Structure of PDB 6m8p Chain U Binding Site BS02

Receptor Information
>6m8p Chain U (length=861) 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
EYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASIGGGGVDVKTMMNTW
TLQKGFPLITITVRGRNVHMKQEHYMKGDTGYLWHVPLTFITSKSDMVHR
FLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHT
AVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNE
LIPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRS
QLLLLACVHNYQPCVQRAEGYFRKWKESNGNLSLPVDVTLAVFAVGAQST
EGWDFLYSKYQFSLSSTEKSQIEFALCRTQNKEKLQWLLDESFKGDKIKT
QEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTT
NQFSTRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNFDKI
RVWLQSEKLER
Ligand information
Ligand IDP52
InChIInChI=1S/C27H37N4O4P/c1-18(2)14-21(17-36(34,35)25(28)13-12-19-8-4-3-5-9-19)27(33)31-24(26(29)32)15-20-16-30-23-11-7-6-10-22(20)23/h3-11,16,18,21,24-25,30H,12-15,17,28H2,1-2H3,(H2,29,32)(H,31,33)(H,34,35)/t21-,24+,25-/m1/s1
InChIKeyQKFOTLXPIIESQI-IEZKXTBUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)C[C@H](CP(=O)([C@H](CCc1ccccc1)N)O)C(=O)N[C@@H](Cc2c[nH]c3c2cccc3)C(=O)N
ACDLabs 12.01O=P(O)(C(N)CCc1ccccc1)CC(C(=O)NC(C(=O)N)Cc3c2ccccc2nc3)CC(C)C
OpenEye OEToolkits 1.7.6CC(C)CC(CP(=O)(C(CCc1ccccc1)N)O)C(=O)NC(Cc2c[nH]c3c2cccc3)C(=O)N
CACTVS 3.370CC(C)C[C@H](C[P](O)(=O)[C@@H](N)CCc1ccccc1)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(N)=O
CACTVS 3.370CC(C)C[CH](C[P](O)(=O)[CH](N)CCc1ccccc1)C(=O)N[CH](Cc2c[nH]c3ccccc23)C(N)=O
FormulaC27 H37 N4 O4 P
NameNalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide
ChEMBLCHEMBL3416733
DrugBank
ZINCZINC000098209288
PDB chain6m8p Chain U Residue 1003 [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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PDB6m8p Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism.
Resolution3.31 Å
Binding residue
(original residue number in PDB)		E183 S316 G317 A318 E320 H353 E354 E376 F433 Y438 S844
Binding residue
(residue number reindexed from 1)		E134 S267 G268 A269 E271 H304 E305 E327 F384 Y389 S790
Annotation score1
Binding affinityBindingDB: IC50=33nM
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:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6m8p, PDBe:6m8p, PDBj:6m8p
PDBsum6m8p
PubMed34489420
UniProtQ9NZ08|ERAP1_HUMAN Endoplasmic reticulum aminopeptidase 1 (Gene Name=ERAP1)

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