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- PDB-7b1o: Crystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in ... -

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Basic information

Entry
Database: PDB / ID: 7b1o
TitleCrystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in complex with compound 22
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsIMMUNOSUPPRESSANT / Enzyme
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 / 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 / negative regulation of T cell proliferation / 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-SLW / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsLammens, A. / Krapp, S. / Lewis, R.T. / Hamilton, M.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of IACS-9779 and IACS-70465 as Potent Inhibitors Targeting Indoleamine 2,3-Dioxygenase 1 (IDO1) Apoenzyme.
Authors: Hamilton, M.M. / Mseeh, F. / McAfoos, T.J. / Leonard, P.G. / Reyna, N.J. / Harris, A.L. / Xu, A. / Han, M. / Soth, M.J. / Czako, B. / Theroff, J.P. / Mandal, P.K. / Burke, J.P. / Virgin- ...Authors: Hamilton, M.M. / Mseeh, F. / McAfoos, T.J. / Leonard, P.G. / Reyna, N.J. / Harris, A.L. / Xu, A. / Han, M. / Soth, M.J. / Czako, B. / Theroff, J.P. / Mandal, P.K. / Burke, J.P. / Virgin-Downey, B. / Petrocchi, A. / Pfaffinger, D. / Rogers, N.E. / Parker, C.A. / Yu, S.S. / Jiang, Y. / Krapp, S. / Lammens, A. / Trevitt, G. / Tremblay, M.R. / Mikule, K. / Wilcoxen, K. / Cross, J.B. / Jones, P. / Marszalek, J.R. / Lewis, R.T.
History
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: 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)93,1704
Polymers92,3282
Non-polymers8422
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
  • dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint1 kcal/mol
Surface area31100 Å2
Methodgel filtration
Unit cell
Length a, b, c (Å)84.560, 91.526, 130.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 46164.062 Da / Num. of mol.: 2 / Fragment: >#FRAGMENT#<
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-SLW / 4-chloranyl-N-[(1R)-1-[(1S,5R)-3-quinolin-4-yloxy-6-bicyclo[3.1.0]hexanyl]propyl]benzamide / 4-chloranyl-~{N}-[(1~{R})-1-[(1~{S},5~{R})-3-quinolin-4-yloxy-6-bicyclo[3.1.0]hexanyl]propyl]benzamide


Mass: 420.931 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 mM Tris pH 8.0, 18% (w/v) PEG6000, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999999701977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999701977 Å / Relative weight: 1
ReflectionResolution: 2.58→74.89 Å / Num. obs: 32082 / % possible obs: 98.7 % / Redundancy: 5 % / Rmerge(I) obs: 5.1 / Net I/σ(I): 5.41
Reflection shellResolution: 2.58→10 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.42 / Num. unique obs: 307900 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.58→74.89 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.877 / SU ML: 0.208 / SU R Cruickshank DPI: 0.5222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.507 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 857 2.7 %RANDOM
Rwork0.2165 ---
obs0.2172 31225 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 137.5 Å2 / Biso mean: 68.596 Å2 / Biso min: 35.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.99 Å2
Refinement stepCycle: final / Resolution: 2.58→74.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 0 60 39 6048
Biso mean--49.01 55.99 -
Num. residues----750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226060
X-RAY DIFFRACTIONr_bond_other_d0.0020.025535
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9748231
X-RAY DIFFRACTIONr_angle_other_deg0.935312809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4065750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14524.023261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5121531
X-RAY DIFFRACTIONr_chiral_restr0.0660.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021238
X-RAY DIFFRACTIONr_nbd_refined0.1910.21294
X-RAY DIFFRACTIONr_nbd_other0.1360.25239
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22953
X-RAY DIFFRACTIONr_nbtor_other0.0750.23125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.210
LS refinement shellResolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 56 -
Rwork0.313 2011 -
all-2067 -
obs--87.36 %
Refinement TLS params.

Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / 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)
14.7792-0.687-1.74243.52011.28413.6128-0.22130.294-0.52130.0326-0.37490.83260.3257-1.22590.59610.0951-0.033-0.00950.6679-0.10470.3937
23.6757-0.5793-1.82671.80660.75923.2796-0.03590.0742-0.1922-0.0679-0.1840.13520.0661-0.37690.21990.03680.0287-0.0360.1323-0.01670.1108
33.6578-4.4908-1.97248.21273.12865.5316-0.097-0.76580.34690.26330.2168-0.2353-0.18440.3623-0.11970.0546-0.0369-0.0530.3619-0.10440.1511
45.28790.49551.99152.32230.14442.7529-0.38420.90760.268-0.0374-0.0033-0.3424-0.17770.87060.38740.1448-0.1069-0.08070.31070.17170.2694
54.36810.97892.4271.33610.35832.9613-0.17090.20710.0549-0.0025-0.0310.0113-0.05520.14480.20190.0924-0.0389-0.01270.0780.06260.1305
64.0608-1.97933.93082.048-1.53048.797-0.0878-1.2822-0.0570.51360.10980.0619-0.1437-1.2954-0.02190.234-0.19910.02990.65390.02850.2545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 107
2X-RAY DIFFRACTION2A108 - 335
3X-RAY DIFFRACTION3A336 - 401
4X-RAY DIFFRACTION4B11 - 107
5X-RAY DIFFRACTION5B108 - 335
6X-RAY DIFFRACTION6B336 - 403

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