Structure of PDB 4flk Chain A Binding Site BS03

Receptor Information
>4flk Chain A (length=304) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKL
LSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCY
PSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHG
DLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHA
QANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMI
CEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARP
HFMS
Ligand information
Ligand IDY10
InChIInChI=1S/C21H31NO5/c1-21(2,3)10-9-16(23)17(24)18(25)19(27-4)20(26)22-15-11-13-7-5-6-8-14(13)12-15/h5-10,15-19,23-25H,11-12H2,1-4H3,(H,22,26)/b10-9+/t16-,17+,18-,19-/m1/s1
InChIKeyXTHOIFAGDPGJPZ-PQQJDVFMSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CO[C@H]([C@H](O)[C@@H](O)[C@H](O)/C=C/C(C)(C)C)C(=O)NC1Cc2ccccc2C1
OpenEye OEToolkits 1.7.6CC(C)(C)C=CC(C(C(C(C(=O)NC1Cc2ccccc2C1)OC)O)O)O
OpenEye OEToolkits 1.7.6CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NC1Cc2ccccc2C1)OC)O)O)O
CACTVS 3.370CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NC1Cc2ccccc2C1
ACDLabs 12.01O=C(NC2Cc1ccccc1C2)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
FormulaC21 H31 N O5
Name(E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
ChEMBLCHEMBL1738933
DrugBank
ZINCZINC000066166121
PDB chain4flk Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4flk Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases.
Resolution1.47 Å
Binding residue
(original residue number in PDB)		Y195 H212 D229 D240 C301 H303 F309 H310 E336 E367
Binding residue
(residue number reindexed from 1)		Y106 H123 D140 D151 C212 H214 F220 H221 E247 E278
Annotation score1
Binding affinityMOAD: ic50=5.58uM
PDBbind-CN: -logKd/Ki=5.25,IC50=5.58uM
BindingDB: IC50=5580nM
Enzymatic activity
Catalytic site (original residue number in PDB) D229 D240 H303 H310 E336 E367
Catalytic site (residue number reindexed from 1) D140 D151 H214 H221 E247 E278
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:4flk, PDBe:4flk, PDBj:4flk
PDBsum4flk
PubMed22913487
UniProtP53582|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)

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