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- PDB-7rrc: IDO1 IN COMPLEX WITH COMPOUND 14 -

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Basic information

Entry
Database: PDB / ID: 7rrc
TitleIDO1 IN COMPLEX WITH COMPOUND 14
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / INDOLEAMINE DIOXYGENASE / HEME / INHIBITOR
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
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-6RI / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLesburg, C.A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2022
Title: Oxetane Promise Delivered: Discovery of Long-Acting IDO1 Inhibitors Suitable for Q3W Oral or Parenteral Dosing.
Authors: Li, D. / Sloman, D.L. / Achab, A. / Zhou, H. / McGowan, M.A. / White, C. / Gibeau, C. / Zhang, H. / Pu, Q. / Bharathan, I. / Hopkins, B. / Liu, K. / Ferguson, H. / Fradera, X. / Lesburg, C.A. ...Authors: Li, D. / Sloman, D.L. / Achab, A. / Zhou, H. / McGowan, M.A. / White, C. / Gibeau, C. / Zhang, H. / Pu, Q. / Bharathan, I. / Hopkins, B. / Liu, K. / Ferguson, H. / Fradera, X. / Lesburg, C.A. / Martinot, T.A. / Qi, J. / Song, Z.J. / Yin, J. / Zhang, H. / Song, L. / Wan, B. / DAddio, S. / Solban, N. / Miller, J.R. / Zamlynny, B. / Bass, A. / Freeland, E. / Ykoruk, B. / Hilliard, C. / Ferraro, J. / Zhai, J. / Knemeyer, I. / Otte, K.M. / Vincent, S. / Sciammetta, N. / Pasternak, A. / Bennett, D.J. / Han, Y.
History
DepositionAug 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)89,6034
Polymers88,7102
Non-polymers8932
Water3,621201
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8012
Polymers44,3551
Non-polymers4461
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)44,8012
Polymers44,3551
Non-polymers4461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.950, 91.339, 129.223
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
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-6RI / N-(4-fluorophenyl)-3-{4-[4-(hydroxymethyl)-6-(trifluoromethyl)pyridin-3-yl]phenyl}oxetane-3-carboxamide


Mass: 446.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H18F4N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 MM TRIS PH 8.0, 20% (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: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.18→74.59 Å / Num. obs: 50323 / % possible obs: 94.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 59.436 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.035 / Rsym value: 0.029 / Χ2: 0.996 / Net I/σ(I): 22.24
Reflection shellResolution: 2.18→2.43 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.29 / Num. unique obs: 14220 / CC1/2: 0.999 / Rrim(I) all: 0.516 / Rsym value: 0.433 / % possible all: 97.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→74.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 11.919 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1423 2.8 %RANDOM
Rwork0.1865 ---
obs0.1873 48900 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.52 Å2 / Biso mean: 61.531 Å2 / Biso min: 35.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-0 Å2
2--1.66 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 2.18→74.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 64 201 6207
Biso mean--50.15 57.74 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196153
X-RAY DIFFRACTIONr_bond_other_d0.0040.025848
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9748364
X-RAY DIFFRACTIONr_angle_other_deg0.937313421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2215763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46824.067268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.546151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7491532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
LS refinement shellResolution: 2.18→2.237 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 87 -
Rwork0.289 3706 -
all-3793 -
obs--97.86 %
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)
14.24540.30741.13972.93670.13092.5376-0.20080.66450.136-0.1078-0.0023-0.2555-0.14110.53340.20310.0676-0.0673-0.02530.19030.12390.26290.57721.83525.954
23.51580.941.78971.02020.29632.2519-0.13220.17910.078-0.0239-0.03550.0583-0.09490.09240.16780.0813-0.0249-0.01240.03310.03990.169671.54516.16122.892
34.2707-2.0073.12261.5327-2.63047.3444-0.2461-0.71170.19960.44370.04140.0105-0.5573-0.36620.20470.2261-0.16940.0530.348-0.06170.268361.73312.33734.937
43.8188-0.7955-1.66972.58170.83493.7276-0.16630.3422-0.526-0.0135-0.28640.57490.2629-0.8290.45280.0707-0.0235-0.01190.3609-0.07810.389941.90742.7417.592
53.2741-0.5427-1.61881.41830.70422.1783-0.05570.0221-0.2212-0.0006-0.12360.05160.103-0.18270.17920.05790.0363-0.02540.0732-0.01110.158361.00944.10812.753
63.668-3.4145-1.70686.70113.53754.8367-0.1249-0.52450.17040.23010.2043-0.17210.10370.244-0.07950.05330.0081-0.06150.1442-0.02930.180970.87753.2620.695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B11 - 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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