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- PDB-8fur: Crystal structure of human IDO1 with compound 11 -

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Basic information

Entry
Database: PDB / ID: 8fur
TitleCrystal structure of human IDO1 with compound 11
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/INHIBITOR / Indoleamine-2 / 3-dioxygenase / tryptophan catabolism / kynurenine / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / positive regulation of T cell apoptotic process / negative 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
Chem-Y9X / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsCritton, D.A. / Lewis, H.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Synthesis and biological evaluation of biaryl alkyl ethers as inhibitors of IDO1.
Authors: Markwalder, J.A. / Balog, A.J. / Williams, D.K. / Nara, S.J. / Reddy, R. / Roy, S. / Kanyaboina, Y. / Li, X. / Johnston, K. / Fan, Y. / Lewis, H. / Marsilio, F. / Yan, C. / Critton, D. / ...Authors: Markwalder, J.A. / Balog, A.J. / Williams, D.K. / Nara, S.J. / Reddy, R. / Roy, S. / Kanyaboina, Y. / Li, X. / Johnston, K. / Fan, Y. / Lewis, H. / Marsilio, F. / Yan, C. / Critton, D. / Newitt, J.A. / Traeger, S.C. / Wu, D.R. / Jure-Kunkel, M.N. / Jayaraman, L. / Lin, T.A. / Sinz, M.W. / Hunt, J.T. / Seitz, S.P.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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
C: Indoleamine 2,3-dioxygenase 1
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,5488
Polymers182,6664
Non-polymers1,8824
Water5,711317
1
A: Indoleamine 2,3-dioxygenase 1
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2744
Polymers91,3332
Non-polymers9412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Indoleamine 2,3-dioxygenase 1
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2744
Polymers91,3332
Non-polymers9412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.882, 120.287, 100.821
Angle α, β, γ (deg.)90.00, 119.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 45666.480 Da / Num. of mol.: 4
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-Y9X / N-(4-methylphenyl)-N'-[(1P,2'P)-4-propoxy-5-propyl-2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-yl]urea


Mass: 470.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate tribasic pH 7.0, 21% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.285→19.76 Å / Num. obs: 54213 / % possible obs: 88.6 % / Redundancy: 3.7 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 2.285→2.62 Å / Redundancy: 3.03 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2708 / CC1/2: 0.537 / % possible all: 45.3

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Processing

Software
NameClassification
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.285→19.76 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.857 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.844 / SU Rfree Blow DPI: 0.37
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2999 2839 5.24 %RANDOM
Rwork0.279 ---
obs0.28 54213 56.6 %-
Displacement parametersBiso mean: 61.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.4174 Å20 Å2-0.2975 Å2
2--6.4833 Å20 Å2
3----3.0658 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.285→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11124 0 140 317 11581
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00722454HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8440545HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6510SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3576HARMONIC5
X-RAY DIFFRACTIONt_it11540HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion17.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16521SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.48 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4236 -5.62 %
Rwork0.3954 1024 -
all0.397 1085 -
obs--5.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22320.1583-0.47332.09831.09875.29520.16420.0429-0.07610.10430.0967-0.1662-0.1968-0.0153-0.2609-0.3218-0.0514-0.0444-0.21580.0746-0.2344-29.766511.16297.5733
23.5112-0.7345-2.37771.63330.68633.0476-0.32870.032-0.06630.14740.111-0.08060.2567-0.08460.2177-0.2683-0.0158-0.0505-0.17810.0736-0.3442-33.648349.070214.7614
32.7396-0.15920.46465.73211.21442.620.06590.2731-0.13660.6344-0.0211-0.84880.43410.0176-0.0448-0.1684-0.0596-0.091-0.1465-0.0319-0.220610.98954.071432.7839
43.80491.52120.6775.5385-0.39921.91720.11320.16130.458-0.2756-0.04661.05-0.15270.2328-0.0666-0.2361-0.0652-0.0847-0.1694-0.0049-0.07443.279966.703352.69
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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