2G6P

Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with Pyridyl pyrimidine derivative

• PDB DOI: https://doi.org/10.2210/pdb2G6P/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-24 Released: 2006-06-20 
• Deposition Author(s): Addlagatta, A., Hu, X., Liu, J.O., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Identification of Pyridinylpyrimidines as Inhibitors of Human Methionine Aminopeptidases.

Hu, X., Addlagatta, A., Matthews, B.W., Liu, J.O.

(2006) Angew Chem Int Ed Engl 45: 3772-3775

• PubMed: 16724298 
• DOI: https://doi.org/10.1002/anie.200600757
• Primary Citation of Related Structures:  
  2G6P

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Organizational Affiliation: 

Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.05 kDa 
• Atom Count: 2,623 
• Modelled Residue Count: 304 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 1	A	304	Homo sapiens	Mutation(s): 0  Gene Names: METAP1, KIAA0094 EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P53582 (Homo sapiens) Explore P53582  Go to UniProtKB:  P53582
PHAROS:  P53582 GTEx:  ENSG00000164024

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HM2	F [auth A]	5-CHLORO-6-METHYL-N-(2-PHENYLETHYL)-2-PYRIDIN-2-YLPYRIMIDIN-4-AMINE C18 H17 Cl N4 HIUOABSWQSUEGK-UHFFFAOYSA-N
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO	B [auth A], C [auth A], D [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HM2	PDBBind:  2G6P	IC50: 600 (nM) from 1 assay(s)
	BindingDB:  2G6P	IC50: min: 700, max: 860 (nM) from 2 assay(s)
		EC50: min: 190, max: 1.50e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.386	α = 90
b = 77.522	β = 90.82
c = 47.72	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-20 
Deposition Author(s): Addlagatta, A., Hu, X., Liu, J.O., Matthews, B.W.

Revision History  

• Version 1.0: 2006-06-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations