Macromolecule Content

Total Structure Weight: 68.21 kDa
Atom Count: 4973
Residue Count: 601
Unique protein chains: 1

6RJ2

Crystal structure of PHGDH in complex with compound 40

DOI: 10.2210/pdb6RJ2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-26 Released: 2019-08-07
Deposition Author(s): Bader, G., Wolkerstorfer, B., Zoephel, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228
R-Value Work: 0.194
R-Value Observed: 0.196

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

PubMed: 31365252 Search on PubMed
DOI: 10.1021/acs.jmedchem.9b00718
Primary Citation of Related Structures:
6CWA, 6RIH, 6RJ6, 6RJ3, 6RJ2, 6RJ5

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A, B	314	Homo sapiens	Mutation(s): 0 Gene Names: PHGDH, PGDH3 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 GTEx: ENSG00000092621
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K52 Query on K52 Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [B] MOL2 format, chain D [A] MOL2 format, chain E [B]	A, B	~{N}-[(1~{R})-1-[4-(ethanoylsulfamoyl)phenyl]ethyl]-2-methyl-5-phenyl-pyrazole-3-carboxamide C₂₁ H₂₂ N₄ O₄ S ALORMMGXOAQIFS-CQSZACIVSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [A] MOL2 format, chain C [A]	A	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
K52	IC50: 100 nM Binding MOAD

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.003	α = 90
b = 110.369	β = 91.62
c = 65.679	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2019-04-26
Released Date: 2019-08-07

Deposition Author(s):

Wolkerstorfer, B.

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.