Structure of PDB 4fyr Chain A Binding Site BS02

Receptor Information
>4fyr Chain A (length=903) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCK
EATDVIIIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVV
HLKGSLVKDSQYEMDSEFEGELADDLAGFYRSEYMEGNVRKVVATTQMQA
ADARKSFPCFDEPAMKAEFNITLIHPKDLTALSNMLPKGPSTPLPEDPNW
NVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWARPSAIAAGHG
DYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRE
NSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFA
SYVEYLGADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINT
PAQISELFDAISYSKGASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIY
LNLWDHLQEAVNNRSIQLPTTVRDIMNRWTLQMGFPVITVDTSTGTLSQE
HFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDVRAQNDLFST
SGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIIND
AFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEV
YGPMKNYLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNG
VPECEEMVSGLFKQWMENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWE
QFRNATLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRKQDATSTII
SITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQAVTRRFSTEYE
LQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTE
NSK
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 chain4fyr Chain A Residue 1014 [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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PDB4fyr The X-ray Crystal Structure of Human Aminopeptidase N Reveals a Novel Dimer and the Basis for Peptide Processing.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		A353 H388 E389 H392 E411 S469 F472 Y477 G894 S895
Binding residue
(residue number reindexed from 1)		A289 H324 E325 H328 E347 S405 F408 Y413 G830 S831
Annotation score3
Binding affinityBindingDB: IC50=20120nM,Ki=2370nM
Enzymatic activity
Catalytic site (original residue number in PDB) E355 H388 E389 H392 E411 S469 Y477
Catalytic site (residue number reindexed from 1) E291 H324 E325 H328 E347 S405 Y413
Enzyme Commision number 3.4.11.2: membrane alanyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0004177 aminopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0038023 signaling receptor activity
GO:0042277 peptide binding
GO:0046872 metal ion binding
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0001525 angiogenesis
GO:0006508 proteolysis
GO:0030154 cell differentiation
GO:0043171 peptide catabolic process
GO:0046718 symbiont entry into host cell
Cellular Component
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005765 lysosomal membrane
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0030667 secretory granule membrane
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4fyr, PDBe:4fyr, PDBj:4fyr
PDBsum4fyr
PubMed22932899
UniProtP15144|AMPN_HUMAN Aminopeptidase N (Gene Name=ANPEP)

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