Structure of PDB 5cbm Chain A Binding Site BS04

Receptor Information

>5cbm Chain A (length=519) Species: 1036723 (Plasmodium falciparum Vietnam Oak-Knoll (FVO))

ASEVPQVVSLDPTSIPIEYNTPIHDIKVQVYDIKGGCNVEEGLTIFLVNN
PGKENGPVKISSKVNDKQVSEFLKDENMEKFNVKLGTSKHFYMFNDNKNS
VAVGYVGCGSVADLSEADMKRVVLSLVTMLHDNKLSKLTVVFEINVDKNL
FRFFLETLFYEYMTDERFKSTDKNVNMEYIKHLGVYINNADTYKEEVEKA
RVYYFGTYYASQLIAAPSNYCNPVSLSNAAVELAQKLNLEYKILGVKELE
ELKMGAYLSVGKGSMYPNKFIHLTYKSKGDVKKKIALVGKGITFDSGGYN
LKAAPGSMIDLMKFDMSGCAAVLGCAYCVGTLKPENVEIHFLSAVCENMV
SKNSYRPGDIITASNGKTIEVGNTDAEGRLTLADALVYAEKLGVDYIVDI
ATLTGAMLYSLGTSYAGVFGNNEELINKILQSSKTSNEPVWWLPIINEYR
ATLNSKYADINQISSSVKASSIVASLFLKEFVQNTAWAHIDIAGVSWNFK
ARKPKGFGVRLLTEFVLND

Ligand information

• Ligand ID: 4ZN
• InChI: InChI=1S/C14H22NO4P/c1-10(2)8-12(14(16)17)9-20(18,19)13(15)11-6-4-3-5-7-11/h3-7,10,12-13H,8-9,15H2,1-2H3,(H,16,17)(H,18,19)/t12-,13-/m1/s1
• InChIKey: RUYPIGFYJMPICK-CHWSQXEVSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CC(C)CC(CP(=O)(C(c1ccccc1)N)O)C(=O)O
  ACDLabs 12.01: NC(c1ccccc1)P(CC(CC(C)C)C(=O)O)(O)=O
  CACTVS 3.385: CC(C)C[C@H](C[P](O)(=O)[C@@H](N)c1ccccc1)C(O)=O
  OpenEye OEToolkits 1.9.2: CC(C)C[C@H](CP(=O)([C@H](c1ccccc1)N)O)C(=O)O
  CACTVS 3.385: CC(C)C[CH](C[P](O)(=O)[CH](N)c1ccccc1)C(O)=O
• Formula: C14 H22 N O4 P
• Name: (2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid
• ZINC: ZINC000012888865
• PDB chain: 5cbm Chain A Residue 704

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cbm Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): K374 D379 K386 M396 F398 D399 D459 E461 T486 T488 G489 A577
• Binding residue (residue number reindexed from 1): K290 D295 K302 M312 F314 D315 D375 E377 T402 T404 G405 A493
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.77,Ki=17nM

Enzymatic activity

• Catalytic site (original residue number in PDB): K386 R463
• Catalytic site (residue number reindexed from 1): K302 R379
• Enzyme Commision number: 3.4.11.1: leucyl aminopeptidase.

Gene Ontology

Molecular Function

• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding
• GO:0070006 metalloaminopeptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0019538 protein metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5cbm, PDBe:5cbm, PDBj:5cbm
• PDBsum: 5cbm
• PubMed: 26406322
• UniProt: A0A024V0B1