Structure of PDB 4fli Chain A Binding Site BS03

Receptor Information
>4fli 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 IDY16
InChIInChI=1S/C14H26N2O6/c1-14(2,3)6-5-8(17)10(19)11(20)12(22-4)13(21)16-7-9(15)18/h5-6,8,10-12,17,19-20H,7H2,1-4H3,(H2,15,18)(H,16,21)/b6-5+/t8-,10+,11-,12-/m1/s1
InChIKeyAVLHKXXFCITIMH-JXTMJACFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(C)C=CC(C(C(C(C(=O)NCC(=O)N)OC)O)O)O
ACDLabs 12.01O=C(NCC(=O)N)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
OpenEye OEToolkits 1.7.6CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NCC(=O)N)OC)O)O)O
CACTVS 3.370CO[C@H]([C@H](O)[C@@H](O)[C@H](O)\C=C\C(C)(C)C)C(=O)NCC(N)=O
CACTVS 3.370CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NCC(N)=O
FormulaC14 H26 N2 O6
Name(E,2R,3R,4S,5R)-N-(2-azanyl-2-oxidanylidene-ethyl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
ChEMBLCHEMBL1738934
DrugBank
ZINCZINC000066156877
PDB chain4fli 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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PDB4fli Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		P192 Y195 H212 D229 D240 Y300 C301 H303 H310 E336 E367
Binding residue
(residue number reindexed from 1)		P103 Y106 H123 D140 D151 Y211 C212 H214 H221 E247 E278
Annotation score1
Binding affinityMOAD: ic50=3.59uM
PDBbind-CN: -logKd/Ki=5.44,IC50=3.59uM
BindingDB: IC50=3590nM
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:4fli, PDBe:4fli, PDBj:4fli
PDBsum4fli
PubMed22913487
UniProtP53582|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)

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