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

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Basic information

Entry
Database: PDB / ID: 9esc
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 / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-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 / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-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 / cytoplasm / cytosol
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: 1.95 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
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)96,0206
Polymers94,1702
Non-polymers1,8504
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-51 kcal/mol
Surface area30250 Å2
Unit cell
Length a, b, c (Å)84.623, 92.049, 132.253
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
#3: Chemical ChemComp-A1H6R / (~{S})-[(7~{a}~{R})-2-cyclopentyl-5,6,7,7~{a}-tetrahydroimidazo[5,1-b][1,3]thiazol-3-yl]-cyclohexyl-methanol


Mass: 308.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28N2OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→46.02 Å / Num. obs: 102271 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rrim(I) all: 0.108 / Net I/σ(I): 10.8
Reflection shellResolution: 1.76→1.87 Å / Num. unique obs: 16009 / CC1/2: 0.178 / Rrim(I) all: 4.87

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 3785 -RANDOM
Rwork0.2338 ---
obs0.2352 75682 99.7 %-
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.1744 Å20 Å20 Å2
2--0.6747 Å20 Å2
3----0.5003 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.95→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 128 197 6259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086322HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.798593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2201SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1125HARMONIC5
X-RAY DIFFRACTIONt_it6322HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion785SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5364SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion16.5
LS refinement shellResolution: 1.95→1.96 Å
RfactorNum. reflection% reflection
Rfree0.3918 76 -
Rwork0.3883 --
obs0.3885 1514 99.73 %

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