5LYX | pdb_00005lyx

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 5-((R)-1-[1,2,4]Triazolo[1,5-a]pyrimidin-7-yl-pyrrolidin-2-ylmethoxy)-isoquinoline

• PDB DOI: https://doi.org/10.2210/pdb5LYX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-09-29 Released: 2017-08-16 
• Deposition Author(s): Musil, D., Heinrich, T., Lehmann, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Novel reversible methionine aminopeptidase-2 (MetAP-2) inhibitors based on purine and related bicyclic templates.

Heinrich, T., Buchstaller, H.P., Cezanne, B., Rohdich, F., Bomke, J., Friese-Hamim, M., Krier, M., Knochel, T., Musil, D., Leuthner, B., Zenke, F.

(2017) Bioorg Med Chem Lett 27: 551-556

• PubMed: 27998678 
• DOI: https://doi.org/10.1016/j.bmcl.2016.12.019
• Primary Citation Related Structures: 
  5LYW, 5LYX


• PubMed Abstract: 
  

  The natural product fumagillin 1 and derivatives like TNP-470 2 or beloranib 3 bind to methionine aminopeptidase 2 (MetAP-2) irreversibly. This enzyme is critical for protein maturation and plays a key role in angiogenesis. In this paper we describe the synthesis, MetAP-2 binding affinity and structural analysis of reversible MetAP-2 inhibitors. Optimization of enzymatic activity of screening hit 10 (IC ₅₀ : 1μM) led to the most potent compound 27 (IC ₅₀ : 0.038μM), with a concomitant improvement in LLE from 2.1 to 4.2. Structural analysis of these MetAP-2 inhibitors revealed an unprecedented conformation of the His339 side-chain imidazole ring being co-planar sandwiched between the imidazole of His331 and the aryl-ether moiety, which is bound to the purine scaffold. Systematic alteration and reduction of H-bonding capability of this metal binding moiety induced an unexpected 180° flip for the triazolo[1,5-a]pyrimdine bicyclic template.

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Organizational Affiliation: 
• Discovery Technologies, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany. Electronic address: [e-mail].
Discovery Technologies, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.
Process Technologies, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.
Drug Disposition, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.
In Vivo Pharmacology, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.
Project Management, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.
Cellular Pharmacology, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.93 kDa 
• Atom Count: 3,014 
• Modeled Residue Count: 363 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 2	A	378	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7BF	B [auth A]	5-[[(2~{R})-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methoxy]isoquinoline C19 H18 N6 O UCCCEISNAUTIDA-OAHLLOKOSA-N
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.215	α = 90
b = 99.944	β = 90
c = 100.93	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data reduction
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Musil, D., Heinrich, T., Lehmann, M.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations