- PDB-4v25: VER-246608, a novel pan-isoform ATP competitive inhibitor of pyru... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4v25
Title
VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells
Type: RIGAKU RAXIS4 / Detector: IMAGE PLATE / Date: Oct 23, 2012 / Details: OSMIC BLUE
Radiation
Monochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2.6→30 Å / Num. obs: 17281 / % possible obs: 98.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.31 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5
Reflection shell
Resolution: 2.6→2.69 Å / Redundancy: 2.19 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.3 / % possible all: 97.7
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0029
refinement
d*TREK
datareduction
d*TREK
datascaling
AMoRE
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: APO PDK2 Resolution: 2.6→25.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.022 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25619
872
5 %
RANDOM
Rwork
0.19834
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obs
0.20132
16403
98.08 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK