6Q0D | pdb_00006q0d

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.185 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Q0D

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties.

Rai, G.Urban, D.J.Mott, B.T.Hu, X.Yang, S.M.Benavides, G.A.Johnson, M.S.Squadrito, G.L.Brimacombe, K.R.Lee, T.D.Cheff, D.M.Zhu, H.Henderson, M.J.Pohida, K.Sulikowski, G.A.Dranow, D.M.Kabir, M.Shah, P.Padilha, E.Tao, D.Fang, Y.Christov, P.P.Kim, K.Jana, S.Muttil, P.Anderson, T.Kunda, N.K.Hathaway, H.J.Kusewitt, D.F.Oshima, N.Cherukuri, M.Davies, D.R.Norenberg, J.P.Sklar, L.A.Moore, W.J.Dang, C.V.Stott, G.M.Neckers, L.Flint, A.J.Darley-Usmar, V.M.Simeonov, A.Waterson, A.G.Jadhav, A.Hall, M.D.Maloney, D.J.

(2020) J Med Chem 63: 10984-11011

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00916
  • Primary Citation Related Structures: 
    6Q0D, 6Q13

  • PubMed Abstract: 

    Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate, with concomitant oxidation of reduced nicotinamide adenine dinucleotide as the final step in the glycolytic pathway. Glycolysis plays an important role in the metabolic plasticity of cancer cells and has long been recognized as a potential therapeutic target. Thus, potent, selective inhibitors of LDH represent an attractive therapeutic approach. However, to date, pharmacological agents have failed to achieve significant target engagement in vivo , possibly because the protein is present in cells at very high concentrations. We report herein a lead optimization campaign focused on a pyrazole-based series of compounds, using structure-based design concepts, coupled with optimization of cellular potency, in vitro drug-target residence times, and in vivo PK properties, to identify first-in-class inhibitors that demonstrate LDH inhibition in vivo . The lead compounds, named NCATS-SM1440 ( 43 ) and NCATS-SM1441 ( 52 ), possess desirable attributes for further studying the effect of in vivo LDH inhibition.


  • Organizational Affiliation
    • National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States.

Macromolecule Content 

  • Total Structure Weight: 229.26 kDa 
  • Atom Count: 16,383 
  • Modeled Residue Count: 1,986 
  • Deposited Residue Count: 1,992 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chain
A, B, C, D, E
A, B, C, D, E, F
332Homo sapiensMutation(s): 0 
Gene Names: LDHAPIG19
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00338
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI

Query on NAI



Download:Ideal Coordinates CCD File
DA [auth F]
I [auth A]
M [auth B]
Q [auth C]
T [auth D]
DA [auth F],
I [auth A],
M [auth B],
Q [auth C],
T [auth D],
Z [auth E]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
P8M
(Subject of Investigation/LOI)

Query on P8M



Download:Ideal Coordinates CCD File
CA [auth F]
H [auth A]
L [auth B]
P [auth C]
S [auth D]
CA [auth F],
H [auth A],
L [auth B],
P [auth C],
S [auth D],
Y [auth E]
2-{3-[3-(cyclopentylethynyl)-4-fluorophenyl]-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid
C31 H28 F2 N4 O4 S2
KTCLNOGFWLXRFB-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
BA [auth F]
G [auth A]
K [auth B]
O [auth C]
R [auth D]
BA [auth F],
G [auth A],
K [auth B],
O [auth C],
R [auth D],
X [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth F]
J [auth B]
N [auth C]
U [auth E]
V [auth E]
AA [auth F],
J [auth B],
N [auth C],
U [auth E],
V [auth E],
W [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.04α = 90
b = 128.07β = 119.35
c = 104.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description