6RJ6

Crystal structure of PHGDH in complex with BI-4924


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis.

Weinstabl, H.Treu, M.Rinnenthal, J.Zahn, S.K.Ettmayer, P.Bader, G.Dahmann, G.Kessler, D.Rumpel, K.Mischerikow, N.Savarese, F.Gerstberger, T.Mayer, M.Zoephel, A.Schnitzer, R.Sommergruber, W.Martinelli, P.Arnhof, H.Peric-Simov, B.Hofbauer, K.S.Garavel, G.Scherbantin, Y.Mitzner, S.Fett, T.N.Scholz, G.Bruchhaus, J.Burkard, M.Kousek, R.Ciftci, T.Sharps, B.Schrenk, A.Harrer, C.Haering, D.Wolkerstorfer, B.Zhang, X.Lv, X.Du, A.Li, D.Li, Y.Quant, J.Pearson, M.McConnell, D.B.

(2019) J Med Chem 62: 7976-7997

  • DOI: 10.1021/acs.jmedchem.9b00718
  • Primary Citation of Related Structures:  
    6CWA, 6RIH, 6RJ6, 6RJ3, 6RJ2, 6RJ5

  • PubMed Abstract: 
  • Phosphoglycerate dehydrogenase (PHGDH) is known to be the rate-limiting enzyme in the serine synthesis pathway in humans. It converts glycolysis-derived 3-phosphoglycerate to 3-phosphopyruvate in a co-factor-dependent oxidation reaction. Herein, we repor ...

    Phosphoglycerate dehydrogenase (PHGDH) is known to be the rate-limiting enzyme in the serine synthesis pathway in humans. It converts glycolysis-derived 3-phosphoglycerate to 3-phosphopyruvate in a co-factor-dependent oxidation reaction. Herein, we report the discovery of BI-4916 , a prodrug of the co-factor nicotinamide adenine dinucleotide (NADH/NAD + )-competitive PHGDH inhibitor BI-4924 , which has shown high selectivity against the majority of other dehydrogenase targets. Starting with a fragment-based screening, a subsequent hit optimization using structure-based drug design was conducted to deliver a single-digit nanomolar lead series and to improve potency by 6 orders of magnitude. To this end, an intracellular ester cleavage mechanism of the ester prodrug was utilized to achieve intracellular enrichment of the actual carboxylic acid based drug and thus overcome high cytosolic levels of the competitive cofactors NADH/NAD + .


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co. KG , Dr.-Boehringer-Gasse 5-11 , 1121 Vienna , Austria.



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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K5K
Query on K5K

Download Ideal Coordinates CCD File 
A, B
2-[4-[(1~{S})-1-[[4,5-bis(chloranyl)-1,6-dimethyl-indol-2-yl]carbonylamino]-2-oxidanyl-ethyl]phenyl]sulfonylethanoic acid
C21 H20 Cl2 N2 O6 S
CJEJFFCPVBZSIE-OAHLLOKOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K5KIC50:  2   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.137α = 90
b = 111.959β = 90.99
c = 62.505γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Database references