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- PDB-9f5r: Holo IDO with a bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 9f5r
TitleHolo IDO with a bound inhibitor
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Inhibitor / heme
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / positive regulation of type 2 immune response / L-tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / T cell proliferation / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase signature 1. / Indoleamine 2,3-dioxygenase signature 2. / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.694 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SAR and cellular potency optimization of novel heme-binding IDO1 inhibitors
Authors: Cren, S. / Lotz, C. / Mac Sweeney, A. / Lange, R. / Kimmerlin, T.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Indoleamine 2,3-dioxygenase 1
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4349
Polymers94,1702
Non-polymers2,2647
Water6,305350
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1784
Polymers47,0851
Non-polymers1,0933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2565
Polymers47,0851
Non-polymers1,1714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.922, 92.293, 131.637
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Indoleamine 2,3-dioxygenase 1 / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 47085.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli (E. coli) / References: UniProt: P14902, indoleamine 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1H93 / (R)-[1-[2,5-bis(fluoranyl)-4-methoxy-phenyl]-1,2,3-triazol-4-yl]-(6-cyclopropylimidazo[1,5-a]pyrazin-5-yl)methanol


Mass: 398.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16F2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol 0.02 M of each carboxylic acid 0.1 M MES/imidazole pH 6.5. Carboxylic acids 0sodium formate, ammonium acetate, trisodium citrate, sodium potassium l- ...Details: 10% w/v PEG 8000, 20% v/v ethylene glycol 0.02 M of each carboxylic acid 0.1 M MES/imidazole pH 6.5. Carboxylic acids 0sodium formate, ammonium acetate, trisodium citrate, sodium potassium l-tartrate, sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.694→75.57 Å / Num. obs: 82644 / % possible obs: 71.6 % / Redundancy: 10.6 % / CC1/2: 0.994 / Rrim(I) all: 0.155 / Net I/σ(I): 7.7
Reflection shellResolution: 1.694→1.842 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4132 / CC1/2: 0.715 / Rrim(I) all: 1.61

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.694→24.48 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 4164 -RANDOM
Rwork0.2173 ---
obs0.2184 82595 71.7 %-
Displacement parametersBiso mean: 30.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.3791 Å20 Å20 Å2
2--0.4465 Å20 Å2
3----0.0674 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.694→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5998 0 156 350 6504
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016380HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.958670HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2228SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1140HARMONIC5
X-RAY DIFFRACTIONt_it6380HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion788SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5591SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.02
LS refinement shellResolution: 1.694→1.79 Å
RfactorNum. reflection% reflection
Rfree0.3137 81 -
Rwork0.2827 --
obs--9.91 %

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