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- PDB-5ek4: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -

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Basic information

Entry
Database: PDB / ID: 5ek4
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IDO1 / inhibitor / 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5PF / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å
AuthorsWu, S.Y. / Peng, Y.H. / Wu, J.S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1
Authors: Peng, Y.H. / Ueng, S.H. / Tseng, C.T. / Hung, M.S. / Song, J.S. / Wu, J.S. / Liao, F.Y. / Fan, Y.S. / Wu, M.H. / Hsiao, W.C. / Hsueh, C.C. / Lin, S.Y. / Cheng, C.Y. / Tu, C.H. / Lee, L.C. / ...Authors: Peng, Y.H. / Ueng, S.H. / Tseng, C.T. / Hung, M.S. / Song, J.S. / Wu, J.S. / Liao, F.Y. / Fan, Y.S. / Wu, M.H. / Hsiao, W.C. / Hsueh, C.C. / Lin, S.Y. / Cheng, C.Y. / Tu, C.H. / Lee, L.C. / Cheng, M.F. / Shia, K.S. / Shih, C. / Wu, S.Y.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)92,6026
Polymers90,7682
Non-polymers1,8344
Water1,69394
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3013
Polymers45,3841
Non-polymers9172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-23 kcal/mol
Surface area15910 Å2
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3013
Polymers45,3841
Non-polymers9172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.768, 92.357, 129.928
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: 45384.211 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-5PF / (1~{R})-1-cyclohexyl-2-[(5~{S})-6-fluoranyl-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol


Mass: 300.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21FN2O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG, Ammonium Fluoride / PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.64→30 Å / Num. obs: 30572 / % possible obs: 98.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 49.41 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.055 / Net I/av σ(I): 19.022 / Net I/σ(I): 17.9 / Num. measured all: 164703
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.64-2.735.40.44830101.05199.5
2.73-2.845.50.31330321.06399.6
2.84-2.975.60.24130451.04599.4
2.97-3.135.60.20130281.03799.3
3.13-3.335.50.13930491.09999.1
3.33-3.585.40.08930341.09799.1
3.58-3.945.30.06530401.06798.5
3.94-4.515.20.04930691.02198.3
4.51-5.685.30.0430851.01198.2
5.68-305.10.03831801.06296.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.374
Highest resolutionLowest resolution
Rotation28.92 Å2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREP11.2.05phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.64→28.938 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1446 4.74 %
Rwork0.1832 29085 -
obs0.1851 30531 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.18 Å2 / Biso mean: 57.3557 Å2 / Biso min: 24.1 Å2
Refinement stepCycle: final / Resolution: 2.64→28.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 130 94 6123
Biso mean--46.47 50.49 -
Num. residues----745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086185
X-RAY DIFFRACTIONf_angle_d0.9878398
X-RAY DIFFRACTIONf_chiral_restr0.054906
X-RAY DIFFRACTIONf_plane_restr0.0051063
X-RAY DIFFRACTIONf_dihedral_angle_d13.8963673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.638-2.73220.30771430.24592754289795
2.7322-2.84150.29921660.243428683034100
2.8415-2.97070.30881520.24572904305699
2.9707-3.12710.29071470.25112893304099
3.1271-3.32280.27231290.23872938306799
3.3228-3.57890.22621280.20782909303799
3.5789-3.93830.20331470.17282911305899
3.9383-4.50630.19631670.15042903307098
4.5063-5.67050.20271310.15042962309398
5.6705-28.94010.18321360.14783043317997
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)
12.23960.2551-1.97264.8556-3.00983.35850.47441.8454-0.5792-1.1571-0.87770.72480.2892-1.32280.35270.57180.125-0.18130.8338-0.28170.57059.0696-5.36573.4979
23.70471.1063-0.09773.59980.31143.5659-0.27930.5481-0.99230.1024-0.48151.30410.2524-1.17120.72870.4236-0.04340.08540.9786-0.250.826-5.1644-2.602820.2626
34.80590.5348-0.93023.05891.4395.2552-0.02360.3533-0.3060.0953-0.49520.3775-0.0996-1.20890.4160.29650.06790.02120.5836-0.09940.49923.74440.532117.1711
48.0325-2.4167-5.35872.23862.52665.90480.3460.6369-0.0848-0.5865-0.42550.0314-0.3142-0.31650.03470.43030.11650.0230.46150.0840.359125.00432.08663.0587
54.62163.844-2.3774.7936-0.74024.71140.1619-0.60170.06410.4503-0.32590.2798-0.2066-0.12540.16250.34790.04530.00650.5476-0.02780.362411.03797.399927.4404
65.3522-0.9868-1.57382.29433.19644.2886-0.1068-0.5314-0.7980.5068-0.33850.2920.6605-0.33490.40770.5590.0110.07140.47350.1250.649112.753-7.843425.1944
78.3046-0.174-2.85724.9133-1.72038.7727-0.1741-1.2265-1.2650.18850.0578-0.03890.82250.61520.06650.49840.0890.05410.42820.12020.602925.7752-8.352620.8064
83.8688-0.1826-0.99560.978-0.27631.9676-0.0358-0.1241-0.3692-0.2651-0.0652-0.34640.15810.27450.10780.38590.09360.07660.3680.00940.336330.9723-2.35659.663
95.4663-7.1564-5.25099.37446.49858.4588-0.2075-1.15480.38190.5010.5752-0.36810.27120.9512-0.35650.3143-0.0299-0.05550.5077-0.02260.391928.0825.619722.9392
104.48980.83151.66441.97170.06414.5388-0.08460.64520.1839-0.1569-0.0586-0.3931-0.25530.79490.13440.3057-0.0050.02870.41210.07940.431549.7151-25.974823.0981
113.83591.15521.49611.80240.48362.5004-0.08380.1927-0.0947-0.0047-0.0092-0.07860.07390.16240.0920.3022-0.00620.03150.21680.03260.238936.1241-31.565825.1941
124.4584-1.09791.99990.3201-0.43433.85350.0722-0.21270.43370.2054-0.0883-0.1539-0.25250.0350.03890.396-0.0004-0.0150.220.03050.412734.0861-17.492529.2473
132.6754-0.46192.18575.77213.20794.427-0.10720.1111.26050.1916-0.09770.998-0.7437-0.79090.37520.45870.0602-0.04350.37550.08530.579321.0509-20.983525.6079
143.29360.59251.25782.46-0.14492.769-0.0653-0.01440.1721-0.3195-0.0140.30030.0681-0.34960.07410.3298-0.0056-0.02560.2637-0.06280.283816.9502-32.669720.2616
154.1498-1.95335.99222.2487-1.64919.4522-0.1546-1.41540.64290.602-0.31670.27070.0062-1.65910.3220.4858-0.06050.10080.6938-0.07970.456517.2122-31.862135.7217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 33 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 159 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 220 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 240 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 241 through 276 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 277 through 298 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 299 through 353 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 354 through 401 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 72 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 240 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 241 through 276 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 277 through 298 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 353 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 354 through 403 )B0

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