6CWA

CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 AB327Homo 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
NAI
Query on NAI

Download Ideal Coordinates CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
3PG
Query on 3PG

Download Ideal Coordinates CCD File 
A, B
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.11α = 89.64
b = 59.62β = 89.83
c = 63.48γ = 79.36
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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