4JNK Oxidoreductase Oxidoreductase Inhibitor date Mar 15, 2013
title Lactate Dehydrogenase A In Complex With Inhibitor Compound 2
authors C.Eigenbrot, M.Ultsch
compound source
Molecule: L-Lactate Dehydrogenase A Chain
Chain: A, B, C, D
Synonym: Ldh-A, Cell Proliferation-Inducing Gene 19 Protein Muscle Subunit, Ldh-M, Renal Carcinoma Antigen Ny-Ren-59;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ldha, Pig19
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.159 R_Free 0.204
length a length b length c angle alpha angle beta angle gamma
168.246 81.487 120.414 90.00 117.13 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand EPE, LAC, NAI, SO4, ZHK enzyme Oxidoreductase E.C. BRENDA
A, D, C, B

Primary referenceIdentification of substituted 2-thio-6-oxo-1,6-dihydropyrimidines as inhibitors of human lactate dehydrogenase., Dragovich PS, Fauber BP, Corson LB, Ding CZ, Eigenbrot C, Ge H, Giannetti AM, Hunsaker T, Labadie S, Liu Y, Malek S, Pan B, Peterson D, Pitts K, Purkey HE, Sideris S, Ultsch M, Vanderporten E, Wei B, Xu Q, Yen I, Yue Q, Zhang H, Zhang X, Bioorg Med Chem Lett. 2013 Jun 1;23(11):3186-94. doi: 10.1016/j.bmcl.2013.04.001., Epub 2013 Apr 10. PMID:23628333
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (470 Kb) [Save to disk]
  • Biological Unit Coordinates (4jnk.pdb1.gz) 459 Kb
  • LPC: Ligand-Protein Contacts for 4JNK
  • CSU: Contacts of Structural Units for 4JNK
  • Structure Factors (1497 Kb)
  • Retrieve 4JNK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JNK from S2C, [Save to disk]
  • Re-refined 4jnk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JNK in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4JNK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4JNK, from MSDmotif at EBI
  • Fold representative 4jnk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jnk_B] [4jnk_A] [4jnk_C] [4jnk_D] [4jnk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4JNK
  • Community annotation for 4JNK at PDBWiki (http://pdbwiki.org)

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