6SBU | pdb_00006sbu

X-ray Structure of Human LDHA with an Allosteric Inhibitor (Compound 3)

PDB DOI: https://doi.org/10.2210/pdb6SBU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-22 Released: 2020-06-10
Deposition Author(s): Friberg, A., Puetter, V., Nguyen, D., Rehwinkel, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.244 (Depositor), 0.244 (DCC)
R-Value Work:
0.207 (Depositor), 0.211 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Evidence for Isoform-Selective Allosteric Inhibition of Lactate Dehydrogenase A.

Friberg, A., Rehwinkel, H., Nguyen, D., Putter, V., Quanz, M., Weiske, J., Eberspacher, U., Heisler, I., Langer, G.

(2020) ACS Omega 5: 13034-13041

PubMed: 32548488 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsomega.0c00715
Primary Citation Related Structures:
6SBU, 6SBV

PubMed Abstract:
Lactate dehydrogenase A (LDHA) is frequently overexpressed in tumors, thereby sustaining high glycolysis rates, tumor growth, and chemoresistance. High-throughput screening resulted in the identification of phthalimide and dibenzofuran derivatives as novel lactate dehydrogenase inhibitors, selectively inhibiting the activity of the LDHA isoenzyme. Cocrystallization experiments confirmed target engagement in addition to demonstrating binding to a novel allosteric binding site present in all four LDHA subunits of the LDH5 homotetramer.

Organizational Affiliation

Bayer AG, Pharmaceuticals, R&D, Müllerstrasse 178, 13342 Berlin, Germany.

Macromolecule Content

Total Structure Weight: 298.14 kDa
Atom Count: 20,754
Modeled Residue Count: 2,624
Deposited Residue Count: 2,656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D, E A, B, C, D, E, F, G, H	332	Homo sapiens	Mutation(s): 0 Gene Names: LDHA, PIG19 EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P00338 (Homo sapiens) Explore P00338 Go to UniProtKB: P00338
PHAROS: P00338 GTEx: ENSG00000134333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00338
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain J [auth A] MOL2 format, chain O [auth E] MOL2 format, chain J [auth A] mmCIF format, chain O [auth E] mmCIF format, chain J [auth A]	J [auth A], O [auth E]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain J [auth A] Focus chain O [auth E] Interactions & Density Focus chain J [auth A] Focus chain O [auth E]
L5N (Subject of Investigation/LOI) Query on L5N Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth D] SDF format, chain P [auth F] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain N [auth E] SDF format, chain L [auth C] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth D] MOL2 format, chain P [auth F] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain N [auth E] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth D] mmCIF format, chain P [auth F] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain N [auth E] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B]	I [auth A] K [auth B] L [auth C] M [auth D] N [auth E] I [auth A], K [auth B], L [auth C], M [auth D], N [auth E], P [auth F], Q [auth G], R [auth H]	4-[[4-[(5-chloranylthiophen-2-yl)carbonylamino]-1,3-bis(oxidanylidene)isoindol-2-yl]methyl]benzoic acid C₂₁ H₁₃ Cl N₂ O₅ S IOFCJSIYHLICRV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.244 (Depositor), 0.244 (DCC)
R-Value Work: 0.207 (Depositor), 0.211 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.445	α = 90
b = 143.853	β = 90
c = 311.225	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-10
Type: Initial release
Version 1.1: 2020-07-01
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description