5NZO

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.

Unterlass, J.E.Basle, A.Blackburn, T.J.Tucker, J.Cano, C.Noble, M.E.M.Curtin, N.J.

(2018) Oncotarget 9: 13139-13153


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-3-phosphoglycerate dehydrogenase
B, A
195Homo sapiensMutation(s): 0 
Gene Names: PHGDH (PGDH3)
EC: 1.1.1.95
Find proteins for O43175 (Homo sapiens)
Go to Gene View: PHGDH
Go to UniProtKB:  O43175
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EZ
Query on 9EZ

Download SDF File 
Download CCD File 
A, B
2-methyl-5-phenyl-pyrazol-3-amine
C10 H11 N3
KCYRMURRLLYLPU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.391α = 97.05
b = 45.783β = 110.12
c = 54.807γ = 106.65
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC2115/A21421

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence
  • Version 1.2: 2018-04-04
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Data collection, Derived calculations