Structure of PDB 5ykp Chain A Binding Site BS04

Receptor Information
>5ykp Chain A (length=305) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PYRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIK
LLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNC
YPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYH
GDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKH
AQANGFSVVRSYCGHGIHKLMHTAPNVPHYAKNKAVGVMKSGHVFTIEPM
ICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSAR
PHFMS
Ligand information
Ligand IDOVA
InChIInChI=1S/C16H26O5/c1-10(2)6-7-12-15(4,21-12)16(19)13(20-5)11(17)8-9-14(16,3)18/h6,12-13,18-19H,7-9H2,1-5H3/t12-,13-,14-,15+,16-/m1/s1
InChIKeyUOXVFQCRPDLSFN-DGXTUMSLSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C2C(OC)C(O)(C1(OC1C/C=C(/C)C)C)C(O)(C)CC2
OpenEye OEToolkits 1.5.0CC(=CC[C@@H]1[C@@](O1)(C)[C@]2([C@@H](C(=O)CC[C@@]2(C)O)OC)O)C
OpenEye OEToolkits 1.5.0CC(=CCC1C(O1)(C)C2(C(C(=O)CCC2(C)O)OC)O)C
CACTVS 3.341CO[CH]1C(=O)CC[C](C)(O)[C]1(O)[C]2(C)O[CH]2CC=C(C)C
CACTVS 3.341CO[C@@H]1C(=O)CC[C@@](C)(O)[C@@]1(O)[C@@]2(C)O[C@@H]2CC=C(C)C
FormulaC16 H26 O5
Name3,4-DIHYDROXY-2-METHOXY-4-METHYL-3-[2-METHYL-3-(3-METHYL-BUT-2-ENYL) -OXIRANYL]-CYCLOHEXANONE;
OVALICIN
ChEMBL
DrugBankDB04324
ZINCZINC000012504299
PDB chain5ykp Chain A Residue 405 [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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PDB5ykp Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis.
Resolution1.68 Å
Binding residue
(original residue number in PDB)		P192 Y195 H212 Y300 C301 E336
Binding residue
(residue number reindexed from 1)		P104 Y107 H124 Y212 C213 E248
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.05,Ki=0.09uM
Enzymatic activity
Enzyme Commision number 3.4.11.18: methionyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ykp, PDBe:5ykp, PDBj:5ykp
PDBsum5ykp
PubMed30837307
UniProtP53582|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)

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