2G6P

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1304Homo sapiensMutation(s): 0 
Gene Names: METAP1KIAA0094
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53582
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HM2
Query on HM2

Download Ideal Coordinates CCD File 
F [auth A]5-CHLORO-6-METHYL-N-(2-PHENYLETHYL)-2-PYRIDIN-2-YLPYRIMIDIN-4-AMINE
C18 H17 Cl N4
HIUOABSWQSUEGK-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding 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 = 47.386α = 90
b = 77.522β = 90.82
c = 47.72γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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