4R69

Lactate Dehydrogenase in complex with inhibitor compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2014.11.008
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    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
EPE
Query on EPE

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Download CCD File 
A, B, C
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
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
W13
Query on W13

Download SDF File 
Download CCD File 
A, B, C, 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
W13IC50: 60 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.007α = 90.00
b = 80.682β = 96.49
c = 101.983γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release