Crystal structure of PHGDH in complex with compound 9

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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This is version 1.3 of the entry. See complete history


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

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenase
A, B
314Homo sapiensMutation(s): 0 
Gene Names: PHGDHPGDH3
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43175 (Homo sapiens)
Explore O43175 
Go to UniProtKB:  O43175
PHAROS:  O43175
GTEx:  ENSG00000092621 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43175
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
K4T Binding MOAD:  6RIH Kd: 1.05e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.351α = 90
b = 112.041β = 96.04
c = 69.116γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description