5JHU | pdb_00005jhu

Potent, Reversible MetAP2 Inhibitors via FBDD

• PDB DOI: https://doi.org/10.2210/pdb5JHU/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-04-21 Released: 2016-05-25 
• Deposition Author(s): Dougan, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Discovery of potent, reversible MetAP2 inhibitors via fragment based drug discovery and structure based drug design-Part 1.

Cheruvallath, Z., Tang, M., McBride, C., Komandla, M., Miura, J., Ton-Nu, T., Erikson, P., Feng, J., Farrell, P., Lawson, J.D., Vanderpool, D., Wu, Y., Dougan, D.R., Plonowski, A., Holub, C., Larson, C.

(2016) Bioorg Med Chem Lett 26: 2774-2778

• PubMed: 27155900 
• DOI: https://doi.org/10.1016/j.bmcl.2016.04.073
• Primary Citation Related Structures: 
  5JHU, 5JI6


• PubMed Abstract: 
  

  Methionine aminopeptidase 2 (MetAP2) is an enzyme that cleaves an N-terminal methionine residue from a number of newly synthesized proteins. Pre-clinical and clinical studies suggest that MetAP2 inhibitors could be used as a novel treatment for obesity. Herein we describe our use of fragment screening methods and structural biology to quickly identify and elaborate an indazole fragment into a series of reversible MetAP2 inhibitors with <10nM potency, excellent selectivity, and favorable in vitro safety profiles.

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Organizational Affiliation: 
• Medicinal Chemistry, Takeda California, United States.
Biological Sciences, Takeda California, United States.
Computational Sciences, Takeda California, United States.
Structural Biology, Takeda California, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.99 kDa 
• Atom Count: 3,243 
• Modeled Residue Count: 362 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 2	A	369	Homo sapiens	Mutation(s): 0  Gene Names: METAP2, MNPEP, P67EIF2 EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P50579 (Homo sapiens) Explore P50579  Go to UniProtKB:  P50579
PHAROS:  P50579 GTEx:  ENSG00000111142

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6KO	F [auth A]	[(2R)-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methyl 2-methoxybenzoate C18 H19 N5 O3 QRTGQCHFTKWKOO-CYBMUJFWSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.181	α = 90
b = 100.964	β = 90
c = 100.126	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
XFIT	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Dougan, D.R.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary