Structure of PDB 3ebh Chain A Binding Site BS02

Receptor Information
>3ebh Chain A (length=889) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKIHYRKDYKPSGFIINQVTLNINIHDQETIVRSVLDMDISKHNVGEDLV
FDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVI
IHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTA
DKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPPLKPCYLFAVVAGDLKHL
SATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYD
LSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVG
HEYFHQYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVD
LLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILG
EEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLW
FSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGL
INPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDQ
LTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFQ
LTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVL
ADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMR
TLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFEL
YDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPND
IRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKL
WNKLDTKRQELMLNEMNTMLQEPQISNNLKEYLLRLTNK
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 chain3ebh Chain A Residue 1085 [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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PDB3ebh Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase
Resolution1.65 Å
Binding residue
(original residue number in PDB)		E319 V459 G460 A461 E463 H496 E497 H500 E519 Y575 Y580
Binding residue
(residue number reindexed from 1)		E124 V264 G265 A266 E268 H301 E302 H305 E324 Y380 Y385
Annotation score3
Binding affinityMOAD: Ki=478.2nM
PDBbind-CN: -logKd/Ki=6.32,Ki=478.2nM
BindingDB: Ki=190nM,IC50=284nM
Enzymatic activity
Catalytic site (original residue number in PDB) E463 H496 E497 H500 E519 E572 Y580
Catalytic site (residue number reindexed from 1) E268 H301 E302 H305 E324 E377 Y385
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:3ebh, PDBe:3ebh, PDBj:3ebh
PDBsum3ebh
PubMed19196988
UniProtO96935|AMPN_PLAF7 Aminopeptidase N (Gene Name=M1AAP)

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