6PLF

Crystal structure of human PHGDH complexed with Compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells.

Mullarky, E.Xu, J.Robin, A.D.Huggins, D.J.Jennings, A.Noguchi, N.Olland, A.Lakshminarasimhan, D.Miller, M.Tomita, D.Michino, M.Su, T.Zhang, G.Stamford, A.W.Meinke, P.T.Kargman, S.Cantley, L.C.

(2019) Bioorg Med Chem Lett 29: 2503-2510

  • DOI: 10.1016/j.bmcl.2019.07.011
  • Primary Citation of Related Structures:  
    6PLG, 6PLF

  • PubMed Abstract: 
  • Cancer cells reprogram their metabolism to support growth and to mitigate cellular stressors. The serine synthesis pathway has been identified as a metabolic pathway frequently altered in cancers and there has been considerable interest in developing pha ...

    Cancer cells reprogram their metabolism to support growth and to mitigate cellular stressors. The serine synthesis pathway has been identified as a metabolic pathway frequently altered in cancers and there has been considerable interest in developing pharmacological agents to target this pathway. Here, we report a series of indole amides that inhibit human 3-phosphoglycerate dehydrogenase (PHGDH), the enzyme that catalyzes the first committed step of the serine synthesis pathway. Using X-ray crystallography, we show that the indole amides bind the NAD + pocket of PHGDH. Through structure-based optimization we were able to develop compounds with low nanomolar affinities for PHGDH in an enzymatic IC 50 assay. In cellular assays, the most potent compounds inhibited de novo serine synthesis with low micromolar to sub-micromolar activities and these compounds successfully abrogated the proliferation of cancer cells in serine free media. The indole amide series reported here represent an important improvement over previously published PHGDH inhibitors as they are markedly more potent and their mechanism of action is better defined.


    Organizational Affiliation

    Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, United States; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, United States. Electronic address: lcantley@med.cornell.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenase AB314Homo sapiensMutation(s): 0 
Gene Names: PHGDHPGDH3
EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (PDB Primary Data), 1.1.1.37 (PDB Primary Data)
Find proteins for O43175 (Homo sapiens)
Explore O43175 
Go to UniProtKB:  O43175
NIH Common Fund Data Resources
PHAROS:  O43175
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ONV
Query on ONV

Download Ideal Coordinates CCD File 
A, B
4-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid
C22 H20 Cl N3 O7
HSLVBDMYOQHSSR-KBXCAEBGSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ONVIC50:  238   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.202α = 90
b = 126.192β = 99.76
c = 59.504γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references