- PDB-5m7m: Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/EN... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5m7m
Title
Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity
Components
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Keywords
HYDROLASE / ATX / Inhibitor / ENPP2
Function / homology
Function and homology information
Vitamin B5 (pantothenate) metabolism / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...Vitamin B5 (pantothenate) metabolism / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of epithelial cell migration / regulation of cell migration / cell motility / chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / hydrolase activity / immune response / calcium ion binding / extracellular space / zinc ion binding / plasma membrane Similarity search - Function
Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A ...Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily Similarity search - Domain/homology
Chem-7HR / IODIDE ION / : / NICKEL (II) ION / PHOSPHATE ION / THIOCYANATE ION / Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 Similarity search - Component
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98011 Å / Relative weight: 1
Reflection
Resolution: 2.7→78.89 Å / Num. obs: 26178 / % possible obs: 93.5 % / Redundancy: 2.7 % / CC1/2: 0.879 / Rmerge(I) obs: 0.164 / Net I/σ(I): 10.7
Reflection shell
Resolution: 2.7→2.77 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.396 / % possible all: 95.6
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
XDS
datareduction
XDS
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→78.53 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.822 / SU B: 17.37 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28426
1278
5.3 %
RANDOM
Rwork
0.22896
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obs
0.23193
23047
92.92 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å