Structure of PDB 4fll Chain A Binding Site BS03

Receptor Information

>4fll Chain A (length=304) Species: 9606 (Homo sapiens)

YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKL
LSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCY
PSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHG
DLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHA
QANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMI
CEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARP
HFMS

Ligand information

• Ligand ID: YZ6
• InChI: InChI=1S/C25H35NO6/c1-25(2,3)14-12-19(27)21(28)22(29)23(31-4)24(30)26-15-13-18(20-11-8-16-32-20)17-9-6-5-7-10-17/h5-12,14,16,18-19,21-23,27-29H,13,15H2,1-4H3,(H,26,30)/b14-12+/t18-,19-,21+,22-,23-/m1/s1
• InChIKey: WQHBNFLTBJLEJU-VQDAETQCSA-N
• SMILES:
  ACDLabs 12.01: O=C(NCCC(c1occc1)c2ccccc2)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
  CACTVS 3.370: CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NCC[CH](c1occc1)c2ccccc2
  CACTVS 3.370: CO[C@H]([C@H](O)[C@@H](O)[C@H](O)\C=C\C(C)(C)C)C(=O)NCC[C@@H](c1occc1)c2ccccc2
  OpenEye OEToolkits 1.7.6: CC(C)(C)C=CC(C(C(C(C(=O)NCCC(c1ccccc1)c2ccco2)OC)O)O)O
  OpenEye OEToolkits 1.7.6: CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NCC[C@H](c1ccccc1)c2ccco2)OC)O)O)O
• Formula: C25 H35 N O6
• Name: (E,2R,3R,4S,5R)-N-[(3R)-3-(furan-2-yl)-3-phenyl-propyl]-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
• ZINC: ZINC000095576254
• PDB chain: 4fll Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4fll Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): Y195 H212 D229 D240 C301 H303 F309 H310 T311 E336 E367
• Binding residue (residue number reindexed from 1): Y106 H123 D140 D151 C212 H214 F220 H221 T222 E247 E278
• Annotation score: 1
• Binding affinity: MOAD: ic50=5.14uM
  PDBbind-CN: -logKd/Ki=5.29,IC50=5.14uM

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

External links

• PDB: RCSB:4fll, PDBe:4fll, PDBj:4fll
• PDBsum: 4fll
• PubMed: 22913487
• UniProt: P53582|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)