4R69 | pdb_00004r69

Lactate Dehydrogenase in complex with inhibitor compound 13

• PDB DOI: https://doi.org/10.2210/pdb4R69/pdb

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


• Deposited: 2014-08-22 Released: 2014-12-24 
• Deposition Author(s): Eigenbrot, C., Ultsch, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 
  0.228 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Optimization of 5-(2,6-dichlorophenyl)-3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase.

Labadie, S., Dragovich, P.S., Chen, J., Fauber, B.P., Boggs, J., Corson, L.B., Ding, C.Z., Eigenbrot, C., Ge, H., Ho, Q., Lai, K.W., Ma, S., Malek, S., Peterson, D., Purkey, H.E., Robarge, K., Salphati, L., Sideris, S., Ultsch, M., VanderPorten, E., Wei, B., Xu, Q., Yen, I., Yue, Q., Zhang, H., Zhang, X., Zhou, A.

(2014) Bioorg Med Chem Lett 25: 75-82

• PubMed: 25466195 
• DOI: https://doi.org/10.1016/j.bmcl.2014.11.008
• Primary Citation Related Structures: 
  4R68, 4R69


• PubMed Abstract: 
  

  Optimization of 5-(2,6-dichlorophenyl)-3-hydroxy-2-mercaptocyclohex-2-enone using structure-based design strategies resulted in inhibitors with considerable improvement in biochemical potency against human lactate dehydrogenase A (LDHA). These potent inhibitors were typically selective for LDHA over LDHB isoform (4–10 fold) and other structurally related malate dehydrogenases, MDH1 and MDH2 (>500 fold). An X-ray crystal structure of enzymatically most potent molecule bound to LDHA revealed two additional interactions associated with enhanced biochemical potency.

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Organizational Affiliation: 
• Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 151.88 kDa 
• Atom Count: 10,485 
• Modeled Residue Count: 1,300 
• Deposited Residue Count: 1,324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D	331	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	F [auth A], I [auth B], L [auth C], N [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
W13	G [auth A], J [auth B], M [auth C], P [auth D]	(5R)-2-[(2-chlorophenyl)sulfanyl]-5-[2,6-dichloro-3-(tetrahydro-2H-pyran-4-ylamino)phenyl]-3-hydroxycyclohex-2-en-1-one C23 H22 Cl3 N O3 S CJPAFXZVJQAZMQ-CYBMUJFWSA-N
EPE	E [auth A], H [auth B], K [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	O [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free:  0.228 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.007	α = 90
b = 80.682	β = 96.49
c = 101.983	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Eigenbrot, C., Ultsch, M.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description