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- PDB-9fon: Cocrystal structure of Drosophila melangaster TDO with Compound 128 -

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Basic information

Entry
Database: PDB / ID: 9fon
TitleCocrystal structure of Drosophila melangaster TDO with Compound 128
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / heme
Function / homology
Function and homology information


ommochrome biosynthetic process / compound eye pigmentation / Tryptophan catabolism / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / kynurenine metabolic process / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / L-tryptophan catabolic process / protein homotetramerization ...ommochrome biosynthetic process / compound eye pigmentation / Tryptophan catabolism / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / kynurenine metabolic process / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / L-tryptophan catabolic process / protein homotetramerization / heme binding / metal ion binding
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.121 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure-Activity Relationship, cellular potency optimization of novel heme-binding Imidazo[5,1-b]thiazoles, imidazo[1,5-a]pyridines and pyrazines as potent IDO inhibitors devoid of Cyp inhibition
Authors: Cren, S. / Kimmerlin, T. / Pothier, J. / Boss, C. / Lotz-Jenne, C. / Mac Sweeney, A. / Pouzol, L. / Chavanton-Arpel, A.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4946
Polymers86,6092
Non-polymers1,8844
Water1,946108
1
A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,98812
Polymers173,2194
Non-polymers3,7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area25580 Å2
ΔGint-218 kcal/mol
Surface area51370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.543, 119.543, 101.804
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Tryptophan 2,3-dioxygenase / TDO / Protein vermilion / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / ...TDO / Protein vermilion / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / Tryptophan pyrrolase / Tryptophanase


Mass: 43304.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: v, CG5163 / Production host: Escherichia coli (E. coli) / References: UniProt: P20351, tryptophan 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-A1IER / (~{R})-(7-chloranylimidazo[1,5-a]pyridin-5-yl)-(1-phenyl-1,2,3-triazol-4-yl)methanol


Mass: 325.752 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12ClN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen I, condition B12

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0007 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.12→103.5 Å / Num. obs: 42135 / % possible obs: 95.3 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.11 / Net I/σ(I): 11.9
Reflection shellResolution: 2.12→2.24 Å / Rmerge(I) obs: 1.388 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2107 / CC1/2: 0.657 / Rrim(I) all: 1.538 / % possible all: 59.4

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.121→39.13 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.275 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.267 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.207
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2097 -RANDOM
Rwork0.2314 ---
obs0.2326 42126 87.9 %-
Displacement parametersBiso mean: 46.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.3372 Å20 Å20 Å2
2--0.3372 Å20 Å2
3----0.6744 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.121→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5404 0 132 108 5644
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085681HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.87719HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1956SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1026HARMONIC5
X-RAY DIFFRACTIONt_it5681HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion733SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4504SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion16.3
LS refinement shellResolution: 2.121→2.19 Å
RfactorNum. reflection% reflection
Rfree0.3216 32 -
Rwork0.2943 --
obs--18.67 %

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