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- PDB-6x5y: IDO1 in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 6x5y
TitleIDO1 in complex with compound 4
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / INDOLEAMINE DIOXYGENASE / IDO1 / INHIBITOR COMPLEX / OXIDOREDUCTASE / 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 / 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-URJ / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLesburg, C.A. / Lammens, A.
CitationJournal: To Be Published
Title: Utilization of MetID and Structural Data to Guide Placement of Spiro and Fused Cyclopropyl Groups for the Synthesis of Low Dose IDO1 Inhibitors
Authors: Hopkins, B. / Zhang, H. / Bharathan, I. / Li, D. / Pu, Q. / Zhou, H. / Martinot, T. / Fradera, X. / Lammens, A. / Lesburg, C.A. / Ballard, J. / Knemeyer, I. / Otte, K. / Solban, N. / ...Authors: Hopkins, B. / Zhang, H. / Bharathan, I. / Li, D. / Pu, Q. / Zhou, H. / Martinot, T. / Fradera, X. / Lammens, A. / Lesburg, C.A. / Ballard, J. / Knemeyer, I. / Otte, K. / Solban, N. / Vincent, S. / Miller, J.R. / Cheng, M. / Geda, P. / Smotrov, N. / Song, X. / Spacciapoli, P. / Bennett, D.J. / Han, Y.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)89,5174
Polymers88,7102
Non-polymers8072
Water39622
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7592
Polymers44,3551
Non-polymers4031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7592
Polymers44,3551
Non-polymers4031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.940, 92.157, 130.126
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: 44355.102 Da / Num. of mol.: 2 / Fragment: N-TERMINAL TRUNCATED
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-URJ / 4-fluoro-N-{1-[5-(2-methylpyrimidin-4-yl)-5,6,7,8-tetrahydro-1,5-naphthyridin-2-yl]cyclopropyl}benzamide


Mass: 403.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22FN5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 mM Tris pH 8.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.65→75.21 Å / Num. obs: 29971 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rrim(I) all: 0.047 / Rsym value: 0.039 / Net I/σ(I): 19.57
Reflection shellResolution: 2.65→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.79 / Num. unique obs: 6969 / CC1/2: 0.869 / Rrim(I) all: 0.521 / Rsym value: 0.435 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: previously solved complex

Resolution: 2.65→75.21 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 32.399 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.648 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 830 2.8 %RANDOM
Rwork0.2399 ---
obs0.2408 29141 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.81 Å2 / Biso mean: 83.571 Å2 / Biso min: 49.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.6 Å2-0 Å20 Å2
2--2.23 Å2-0 Å2
3---1.37 Å2
Refinement stepCycle: final / Resolution: 2.65→75.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 60 22 6012
Biso mean--65.38 64.75 -
Num. residues----746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195963
X-RAY DIFFRACTIONr_bond_other_d0.0020.025664
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9738106
X-RAY DIFFRACTIONr_angle_other_deg1.109312936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20323.684247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17715959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9221532
X-RAY DIFFRACTIONr_chiral_restr0.0640.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021392
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 63 -
Rwork0.357 2121 -
all-2184 -
obs--99.05 %
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)
15.26080.56851.69133.0097-0.00484.0984-0.21550.7660.1975-0.0404-0.0402-0.3902-0.10140.72060.25570.0996-0.0569-0.05830.20810.11550.152490.53322.04926.524
25.10331.30972.76511.03260.61262.8434-0.07150.07350.04430.054-0.03210.02410.030.00170.10370.1224-0.0311-0.00450.08420.04430.044571.51316.36523.223
36.8601-3.83564.4692.5002-1.743811.0695-0.5235-1.05090.23030.62690.1931-0.1312-0.5337-0.8620.33050.4986-0.37180.00020.67890.03660.194661.8512.67835.192
45.2015-1.1278-1.68773.33111.27454.3035-0.14240.3527-0.53720.0553-0.32770.82020.2388-1.20510.470.07620.0013-0.01830.5441-0.09640.290441.70243.15218.253
54.2552-0.7292-1.98951.38370.76073.3555-0.06020.0827-0.183-0.0277-0.19320.08980.0687-0.35780.25330.04690.0334-0.0150.13-0.03970.029261.05144.3912.949
64.1153-4.1572-2.27298.41833.35645.38650.0286-0.6840.30150.06490.2091-0.0743-0.10990.3453-0.23780.0598-0.0425-0.04370.2011-0.05350.094871.13553.63220.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 107
2X-RAY DIFFRACTION2A108 - 335
3X-RAY DIFFRACTION3A336 - 402
4X-RAY DIFFRACTION4B10 - 107
5X-RAY DIFFRACTION5B108 - 335
6X-RAY DIFFRACTION6B336 - 401

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