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- PDB-5ek2: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -

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Basic information

Entry
Database: PDB / ID: 5ek2
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 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 / stereocilium bundle / tryptophan catabolic process to kynurenine / 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 / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / positive regulation of T cell apoptotic process / Tryptophan catabolism / negative 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
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-5PJ / 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: 2.68 Å
AuthorsPeng, Y.H. / Wu, J.S. / Wu, S.Y.
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)92,5986
Polymers90,7682
Non-polymers1,8304
Water1,65792
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2993
Polymers45,3841
Non-polymers9152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-23 kcal/mol
Surface area16190 Å2
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2993
Polymers45,3841
Non-polymers9152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-24 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.005, 96.985, 131.206
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


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


Mass: 298.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19FN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
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: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.68→30 Å / Num. obs: 30626 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.4 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Χ2: 1.065 / Net I/av σ(I): 19.448 / Net I/σ(I): 16.1 / Num. measured all: 100244
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.783.20.49730540.8160.3170.5911.09598.9
2.78-2.893.30.34830430.90.220.4131.06798.8
2.89-3.023.30.28830620.9340.180.3411.08398.6
3.02-3.183.30.230600.9610.1250.2371.05598.5
3.18-3.383.30.12730480.9840.0790.1511.04698.4
3.38-3.643.30.07730670.9930.0490.0921.05198
3.64-43.30.05230570.9950.0330.0621.06997.2
4-4.583.30.04230310.9960.0270.051.0896.2
4.58-5.763.30.03430910.9970.0220.0411.01296.4
5.76-303.20.02531130.9990.0160.031.09493.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.473
Highest resolutionLowest resolution
Rotation29.49 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
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.68→29.487 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1552 5.07 %
Rwork0.1708 29047 -
obs0.1738 30599 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.3 Å2 / Biso mean: 69.0602 Å2 / Biso min: 38.57 Å2
Refinement stepCycle: final / Resolution: 2.68→29.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5935 0 130 92 6157
Biso mean--52.66 64.6 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016223
X-RAY DIFFRACTIONf_angle_d1.0658453
X-RAY DIFFRACTIONf_chiral_restr0.056911
X-RAY DIFFRACTIONf_plane_restr0.0071074
X-RAY DIFFRACTIONf_dihedral_angle_d19.82288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6799-2.76630.34931520.25472543269596
2.7663-2.86510.29591230.2322675279899
2.8651-2.97970.30011400.2232615275599
2.9797-3.11520.30041430.22812646278999
3.1152-3.27920.27431530.22852646279999
3.2792-3.48440.29761430.20692656279998
3.4844-3.75290.23081290.17132647277698
3.7529-4.12970.22571260.15262633275997
4.1297-4.72510.18311490.13682633278297
4.7251-5.94520.19331570.15052661281897
5.9452-29.48880.19261370.13692692282993
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)
10.4113-0.06540.01210.67760.15020.04210.5507-0.74940.29970.9289-0.69780.42840.2616-0.9624-00.8099-0.15930.0870.9313-0.15980.73338.60365.3974-4.3709
24.31850.18821.06922.1299-0.52374.6594-0.1075-0.05370.2290.0816-0.22740.637-0.033-1.0854-00.5655-0.020.0030.872-0.18810.7121-0.07860.3955-19.4265
33.45650.09020.81790.064-0.42211.24460.257-0.5087-0.1180.52-0.3028-0.05040.2554-0.3389-00.6494-0.082-0.01920.64110.05160.534625.1949-0.9954-3.1494
42.68381.4256-0.42252.1551.3981.27-0.04670.5530.1648-0.2525-0.0980.1692-0.1728-0.2411-00.6649-0.0092-0.01240.7352-0.02640.607512.70492.0169-26.488
51.88020.5498-0.23681.01151.2782.99380.0030.22380.2064-0.0553-0.1219-0.0516-0.32410.175700.628-0.0376-0.05760.51190.03470.574329.69164.9567-13.0171
61.4849-0.357-1.59552.7129-0.20172.132-0.39320.1629-0.3711-0.46780.3435-0.4617-0.16820.2447-00.61680.0130.09820.60550.04490.60831.2358-5.4837-22.9498
74.0627-0.0351-0.68731.5073-0.90341.1718-0.0507-1.0881-0.01550.08680.0393-0.47270.07970.84960.00010.65810.0441-0.00560.74930.11050.700549.516227.9716-24.908
85.6618-0.051-2.03642.66050.76592.9437-0.0314-0.2817-0.2268-0.027-0.1833-0.1571-0.02330.3492-0.00030.55910.02860.04320.44190.09510.538343.703528.7026-28.5009
92.9237-0.9485-1.21361.0610.92210.26910.2212-0.39290.6060.1011-0.0007-0.068-0.34070.010400.70760.0810.03850.59830.03290.617622.541240.3173-17.8345
100.8536-0.30360.05180.29540.48751.30430.02081.1481-0.5059-0.22890.12010.3647-0.1996-0.443300.69030.06870.05980.6746-0.01880.638435.959630.2291-40.9104
111.68471.0011-1.02610.7803-1.2222.0818-0.39580.3115-0.8406-0.1691-0.02770.02560.3739-0.0672-00.72360.00830.12520.5685-0.0220.867833.747519.07-30.5646
120.42480.0405-0.42680.34110.00820.4217-0.3853-0.0639-2.108-0.0688-0.09420.60250.7798-0.70210.00110.7765-0.03330.11890.66-0.03440.945420.555621.698-26.6449
132.30010.0572-0.73271.3143-0.17012.09940.11190.2387-0.2251-0.0118-0.22890.19660.0552-0.2882-00.65070.08260.08960.57690.09330.589816.097333.4396-20.9292
141.91461.39470.42672.0387-1.29092.108-0.21330.8882-0.3739-0.3661-0.31940.10460.3049-0.6762-0.00030.70890.1408-0.06620.9743-0.04310.646117.547331.4238-37.17
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 159 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 220 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 221 through 276 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 277 through 353 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 403 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 72 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 159 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 220 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 221 through 240 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 241 through 276 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 277 through 298 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 299 through 353 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 354 through 403 )B0

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