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- PDB-6pu7: Human IDO1 in complex with compound 17 (N-{2-[(4-{N-[(7S)-4-fluor... -

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Basic information

Entry
Database: PDB / ID: 6pu7
TitleHuman IDO1 in complex with compound 17 (N-{2-[(4-{N-[(7S)-4-fluorobicyclo[4.2.0]octa-1,3,5-trien-7-yl]-N'-hydroxycarbamimidoyl}-1,2,5-oxadiazol-3-yl)sulfanyl]ethyl}acetamide)
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / indoleamine / dioxygenase / heme / 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
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-OY4 / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.43 Å
AuthorsLesburg, C.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Discovery of Amino-cyclobutarene-derived Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitors for Cancer Immunotherapy.
Authors: Zhang, H. / Liu, K. / Pu, Q. / Achab, A. / Ardolino, M.J. / Cheng, M. / Deng, Y. / Doty, A.C. / Ferguson, H. / Fradera, X. / Knemeyer, I. / Kurukulasuriya, R. / Lam, Y.H. / Lesburg, C.A. / ...Authors: Zhang, H. / Liu, K. / Pu, Q. / Achab, A. / Ardolino, M.J. / Cheng, M. / Deng, Y. / Doty, A.C. / Ferguson, H. / Fradera, X. / Knemeyer, I. / Kurukulasuriya, R. / Lam, Y.H. / Lesburg, C.A. / Martinot, T.A. / McGowan, M.A. / Miller, J.R. / Otte, K. / Biju, P.J. / Sciammetta, N. / Solban, N. / Yu, W. / Zhou, H. / Wang, X. / Bennett, D.J. / Han, Y.
History
DepositionJul 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: 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)90,5606
Polymers88,5962
Non-polymers1,9644
Water3,873215
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2803
Polymers44,2981
Non-polymers9822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2803
Polymers44,2981
Non-polymers9822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.427, 96.516, 127.725
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: 44298.051 Da / Num. of mol.: 2 / Fragment: N-terminal truncated (UNP residues 11-402)
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-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-OY4 / N-{2-[(4-{N-[(7S)-4-fluorobicyclo[4.2.0]octa-1,3,5-trien-7-yl]-N'-hydroxycarbamimidoyl}-1,2,5-oxadiazol-3-yl)sulfanyl]ethyl}acetamide


Mass: 365.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16FN5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 59.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: unavailable

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 31, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→77 Å / Num. obs: 39145 / % possible obs: 95.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 46.879 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.09 / Χ2: 0.952 / Net I/σ(I): 11.41
Reflection shellResolution: 2.43→2.68 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.61 / Num. unique obs: 9974 / CC1/2: 0.999 / Rrim(I) all: 0.026 / % possible all: 97.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.43→77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 15.97 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.253
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1064 2.7 %RANDOM
Rwork0.2004 ---
obs0.2017 38080 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.42 Å2 / Biso mean: 45.46 Å2 / Biso min: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2--1.06 Å20 Å2
3---1.51 Å2
Refinement stepCycle: final / Resolution: 2.43→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5946 0 136 215 6297
Biso mean--44.77 39.45 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226229
X-RAY DIFFRACTIONr_bond_other_d0.0020.025632
X-RAY DIFFRACTIONr_angle_refined_deg1.1482.0158486
X-RAY DIFFRACTIONr_angle_other_deg0.93313063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5015763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75324.275269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.144151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5831531
X-RAY DIFFRACTIONr_chiral_restr0.0640.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021234
X-RAY DIFFRACTIONr_nbd_refined0.1660.21280
X-RAY DIFFRACTIONr_nbd_other0.1310.25507
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22965
X-RAY DIFFRACTIONr_nbtor_other0.0760.23058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1250.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.28
LS refinement shellResolution: 2.43→2.493 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 79 -
Rwork0.28 2826 -
all-2905 -
obs--97.03 %
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)
15.2013-0.5346-1.33722.4894-0.29482.4426-0.0883-0.3856-0.23030.0162-0.0553-0.16730.13640.40140.1435-0.16710.0257-0.0141-0.23410.0898-0.05974.24225.016-27.644
24.5294-1.0103-1.87710.61440.20831.3964-0.01180.0025-0.13820.0423-0.03550.1361-0.0275-0.14410.0473-0.07470.0159-0.0084-0.19690.0468-0.1431-15.03729.728-24.392
36.70421.2943-4.31371.7351-1.85988.7601-0.07931.1606-0.3016-0.4789-0.21170.19760.2956-0.76810.2909-0.08730.1047-0.03710.14490.0471-0.0603-25.68232.452-36.137
44.24840.73051.33792.37050.64013.389-0.0744-0.30740.38040.0173-0.34070.5981-0.0985-0.8990.4152-0.11310.01740.01670.0732-0.07770.0144-43.1170.996-17.455
53.41440.67371.60411.18670.84812.0081-0.08710.02390.13640.0159-0.08310.0903-0.114-0.03870.1702-0.1121-0.00650.0251-0.15680.0011-0.1423-23.7211.428-12.264
63.22831.96660.45445.31642.8775.161-0.01080.2332-0.1992-0.16010.0102-0.1431-0.18440.21370.0006-0.15740.04080.0209-0.1805-0.0442-0.1246-12.444-7.25-19.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B10 - 107
2X-RAY DIFFRACTION2B108 - 335
3X-RAY DIFFRACTION3B336 - 402
4X-RAY DIFFRACTION4A10 - 107
5X-RAY DIFFRACTION5A108 - 335
6X-RAY DIFFRACTION6A336 - 401

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