4RLS

Lactate Dehydrogenase in complex with inhibitor compound 47


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of 3,6-disubstituted dihydropyrones as inhibitors of human lactate dehydrogenase.

Fauber, B.P.Dragovich, P.S.Chen, J.Corson, L.B.Ding, C.Z.Eigenbrot, C.Labadie, S.Malek, S.Peterson, D.Purkey, H.E.Robarge, K.Sideris, S.Ultsch, M.Wei, B.Yen, I.Yue, Q.Zhou, A.

(2014) Bioorg.Med.Chem.Lett. 24: 5683-5687

  • DOI: 10.1016/j.bmcl.2014.10.067

  • PubMed Abstract: 
  • A series of 3,6-disubstituted dihydropyrones were identified as inhibitors of human lactate dehydrogenase (LDH)-A. Structure activity relationships were explored and a series of 6,6-spiro analogs led to improvements in LDHA potency (IC50 <350 nM). An ...

    A series of 3,6-disubstituted dihydropyrones were identified as inhibitors of human lactate dehydrogenase (LDH)-A. Structure activity relationships were explored and a series of 6,6-spiro analogs led to improvements in LDHA potency (IC50 <350 nM). An X-ray crystal structure of an improved compound bound to human LDHA was obtained and it illustrated additional opportunities to enhance the potency of these compounds, resulting in the identification of 51 (IC50=30 nM).


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-lactate dehydrogenase A chain
A, B, C, D
331Homo sapiensMutation(s): 0 
Gene Names: LDHA
EC: 1.1.1.27
Find proteins for P00338 (Homo sapiens)
Go to Gene View: LDHA
Go to UniProtKB:  P00338
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAI
Query on NAI

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Download CCD File 
A, B, C, D
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
2OP
Query on 2OP

Download SDF File 
Download CCD File 
B, C
(2S)-2-HYDROXYPROPANOIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-REOHCLBHSA-N
 Ligand Interaction
49C
Query on 49C

Download SDF File 
Download CCD File 
D
(1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one
C19 H15 Cl O3 S
RBPDUTMGGGWCRQ-LJQANCHMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
49CIC50: 360 - 2600 nM (100) BINDINGDB
49CIC50: 360 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.234α = 90.00
b = 81.758β = 98.28
c = 104.563γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references