4FLI

Human MetAP1 with bengamide analog Y16, in Mn form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases.

Xu, W.Lu, J.P.Ye, Q.Z.

(2012) J.Med.Chem. 55: 8021-8027

  • DOI: 10.1021/jm3008695
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Natural-product-derived bengamides possess potent antiproliferative activity and target human methionine aminopeptidases (MetAPs) for their cellular effects. Several derivatives were designed, synthesized, and evaluated as MetAP inhibitors. Here, we ...

    Natural-product-derived bengamides possess potent antiproliferative activity and target human methionine aminopeptidases (MetAPs) for their cellular effects. Several derivatives were designed, synthesized, and evaluated as MetAP inhibitors. Here, we present four new X-ray structures of human MetAP1 in complex with the inhibitors. Together with the previous structures of bengamide derivatives with human MetAP2 and tubercular MtMetAP1c, analysis of the interactions of these inhibitors at the active site provides structural basis for further modification of these bengamide inhibitors for improved potency and selectivity as anticancer and antibacterial therapeutics.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 1
A
326Homo sapiensMutation(s): 0 
Gene Names: METAP1 (KIAA0094)
EC: 3.4.11.18
Find proteins for P53582 (Homo sapiens)
Go to Gene View: METAP1
Go to UniProtKB:  P53582
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Y16
Query on Y16

Download SDF File 
Download CCD File 
A
(E,2R,3R,4S,5R)-N-(2-azanyl-2-oxidanylidene-ethyl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
C14 H26 N2 O6
AVLHKXXFCITIMH-JXTMJACFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y16IC50: 3590 nM (100) BINDINGDB
Y16IC50: 3590 nM BINDINGMOAD
Y16IC50: 3590 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.771α = 90.00
b = 77.562β = 90.18
c = 48.811γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-3000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement
HKL-3000data reduction
HKL-3000data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-14 
  • Released Date: 2012-09-19 
  • Deposition Author(s): Ye, Q.Z., Xu, W.

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description