Structure of PDB 4k5o Chain A Binding Site BS02

Receptor Information

>4k5o Chain A (length=889) Species: 186763 (Plasmodium falciparum FcB1/Columbia)

PKIHYRKDYKPSGFIINQVTLNINIHDQETIVRSVLDMDISKHNVGEDLV
FDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVI
IHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTA
DKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPPLKPCYLFAVVAGDLKHL
SATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYD
LSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVG
HEYFHQYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVD
LLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILG
EEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLW
FSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGL
INPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDQ
LTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFQ
LTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVL
ADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMR
TLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFEL
YDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPND
IRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKL
WNKLDTKRQELMLNEMNTMLQEPQISNNLKEYLLRLTNK

Ligand information

• Ligand ID: 1OT
• InChI: InChI=1S/C10H12N3O3P/c11-10(17(14,15)16)8-2-4-9(5-3-8)13-7-1-6-12-13/h1-7,10H,11H2,(H2,14,15,16)/t10-/m1/s1
• InChIKey: KEKSMECJAGVZSC-SNVBAGLBSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1cnn(c1)c2ccc(cc2)C(N)P(=O)(O)O
  CACTVS 3.370: N[C@@H](c1ccc(cc1)n2cccn2)[P](O)(O)=O
  ACDLabs 12.01: O=P(O)(O)C(c1ccc(cc1)n2nccc2)N
  CACTVS 3.370: N[CH](c1ccc(cc1)n2cccn2)[P](O)(O)=O
  OpenEye OEToolkits 1.7.6: c1cnn(c1)c2ccc(cc2)[C@H](N)P(=O)(O)O
• Formula: C10 H12 N3 O3 P
• Name: {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid
• ZINC: ZINC000096927715
• PDB chain: 4k5o Chain A Residue 1106

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4k5o Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): E319 V459 A461 M462 E463 H496 E497 H500 E519 Y575 Y580 M1034
• Binding residue (residue number reindexed from 1): E124 V264 A266 M267 E268 H301 E302 H305 E324 Y380 Y385 M839
• Annotation score: 1
• Binding affinity: MOAD: Ki=104uM
  PDBbind-CN: -logKd/Ki=3.98,Ki=104uM

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

External links

• PDB: RCSB:4k5o, PDBe:4k5o, PDBj:4k5o
• PDBsum: 4k5o
• PubMed: 23713488
• UniProt: O96935|AMPN_PLAF7 Aminopeptidase N (Gene Name=M1AAP)