7X11

Crystal structure of ME1 in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb7X11/pdb

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

Deposited: 2022-02-22 Released: 2022-07-20
Deposition Author(s): Amano, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.299
R-Value Work: 0.265
R-Value Observed: 0.266

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery and Characterization of a Novel Allosteric Small-Molecule Inhibitor of NADP + -Dependent Malic Enzyme 1.

Yoshida, T., Kawabe, T., Cantley, L.C., Lyssiotis, C.A.

(2022) Biochemistry 61: 1548-1553

PubMed: 35819845 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.2c00123
Primary Citation of Related Structures:
7X11, 7X12

PubMed Abstract:
NADP ⁺-dependent malic enzyme 1 (ME1) decarboxylates malate to form pyruvate and NADPH in the cytoplasm, where it mediates diverse biological functions related to the generation of lipids and other cellular building blocks. As such, ME1 has been implicated in the progression of cancers and has received attention as a promising drug target. Here we report the identification of a novel small-molecule inhibitor of ME1, designated AS1134900. AS1134900 is highly selective for ME1 compared with ME2 and uncompetitively inhibits ME1 activity in the presence of its substrates NADP ⁺ and malate. In addition, X-ray crystal structure analysis of the enzyme-inhibitor complex revealed that AS1134900 binds outside the ME1 active site in a novel allosteric site. Structural comparison of the ME1 quaternary complex with AS1134900, NADPH, and Mn ²⁺, alongside known crystal structures of malic enzymes, indicated the determined crystal ME1-inhibitor complex is in the open form conformation. These results provide insights and a starting point for further discovery of drugs that inhibit ME1 activity in cancer cells.

Organizational Affiliation

Business Development, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.

Macromolecule Content

Total Structure Weight: 261.96 kDa
Atom Count: 18,738
Modelled Residue Count: 2,256
Deposited Residue Count: 2,288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent malic enzyme	A, B, C, D	572	Homo sapiens	Mutation(s): 0 Gene Names: ME1 EC: 1.1.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P48163 (Homo sapiens) Explore P48163 Go to UniProtKB: P48163
PHAROS: P48163 GTEx: ENSG00000065833
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48163
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
86I (Subject of Investigation/LOI) Query on 86I Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	6-[(7-methyl-2-propyl-imidazo[4,5-b]pyridin-4-yl)methyl]-2-[2-(1H-1,2,3,4-tetrazol-5-yl)phenyl]-1,3-benzothiazole C₂₅ H₂₂ N₈ S LGDMZWWVVLGYPR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]