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- PDB-6wpe: HUMAN IDO1 IN COMPLEX WITH COMPOUND 4 -

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Basic information

Entry
Database: PDB / ID: 6wpe
TitleHUMAN IDO1 IN COMPLEX WITH COMPOUND 4
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / 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
Chem-U6G / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLesburg, C.A. / Lammens, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Carbamate and N -Pyrimidine Mitigate Amide Hydrolysis: Structure-Based Drug Design of Tetrahydroquinoline IDO1 Inhibitors.
Authors: Li, D. / Deng, Y. / Achab, A. / Bharathan, I. / Hopkins, B.A. / Yu, W. / Zhang, H. / Sanyal, S. / Pu, Q. / Zhou, H. / Liu, K. / Lim, J. / Fradera, X. / Lesburg, C.A. / Lammens, A. / ...Authors: Li, D. / Deng, Y. / Achab, A. / Bharathan, I. / Hopkins, B.A. / Yu, W. / Zhang, H. / Sanyal, S. / Pu, Q. / Zhou, H. / Liu, K. / Lim, J. / Fradera, X. / Lesburg, C.A. / Lammens, A. / Martinot, T.A. / Cohen, R.D. / Doty, A.C. / Ferguson, H. / Nickbarg, E.B. / Cheng, M. / Spacciapoli, P. / Geda, P. / Song, X. / Smotrov, N. / Abeywickrema, P. / Andrews, C. / Chamberlin, C. / Mabrouk, O. / Curran, P. / Richards, M. / Saradjian, P. / Miller, J.R. / Knemeyer, I. / Otte, K.M. / Vincent, S. / Sciammetta, N. / Pasternak, A. / Bennett, D.J. / Han, Y.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 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)89,5894
Polymers88,7102
Non-polymers8792
Water2,792155
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7942
Polymers44,3551
Non-polymers4391
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)44,7942
Polymers44,3551
Non-polymers4391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.463, 93.499, 131.358
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-U6G / 4-chloro-N-{[1-(3-chlorobenzene-1-carbonyl)-1,2,3,4-tetrahydroquinolin-6-yl]methyl}benzamide


Mass: 439.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20Cl2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3 Å3/Da / Density % sol: 59.06 %
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: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.43→76.17 Å / Num. obs: 39371 / % possible obs: 97.4 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rrim(I) all: 0.04 / Rsym value: 0.033 / Net I/σ(I): 20.2
Reflection shellResolution: 2.43→2.68 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.38 / Num. unique obs: 10045 / CC1/2: 0.87 / Rrim(I) all: 0.403 / Rsym value: 0.327 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: previously solved structure

Resolution: 2.43→76.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 17.46 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.232
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 971 2.4 %RANDOM
Rwork0.1979 ---
obs0.1988 38760 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.28 Å2 / Biso min: 36.58 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å20 Å2-0 Å2
2--1.05 Å20 Å2
3---2 Å2
Refinement stepCycle: final / Resolution: 2.43→76.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5960 0 60 155 6175
Biso mean--46.52 55.32 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196183
X-RAY DIFFRACTIONr_bond_other_d0.0040.025904
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9738394
X-RAY DIFFRACTIONr_angle_other_deg0.899313558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7285766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50324.074270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.538151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4531533
X-RAY DIFFRACTIONr_chiral_restr0.0580.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021447
LS refinement shellResolution: 2.431→2.494 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 73 -
Rwork0.313 2829 -
all-2902 -
obs--97.25 %
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)
15.26630.84631.73622.46770.03541.7598-0.210.73610.2105-0.02960.0691-0.2901-0.03160.56490.14080.1662-0.0326-0.05730.20590.09080.182292.08122.27726.564
23.69771.02181.97291.32240.36052.2914-0.11760.11720.1058-0.009-0.02160.04970.00320.03110.13920.1575-0.0273-0.01930.03350.03820.06972.76116.56223.333
36.3384-2.4983.97821.4264-1.51118.4682-0.1957-0.96780.39990.43850.0452-0.1192-0.5916-0.64420.15050.3593-0.22660.06810.44670.00380.234963.28513.55735.811
44.0446-1.0449-1.56562.46380.97843.3459-0.12680.3562-0.47490.0622-0.31320.73210.1812-0.94570.43990.1588-0.0321-0.00030.4137-0.10210.30642.58543.86218.485
53.2989-0.6416-1.67751.50970.66922.734-0.01690.0863-0.1411-0.0447-0.15280.07520.0444-0.27190.16980.09960.0233-0.04170.0703-0.02680.031162.20745.04513.11
66.4686-5.7493-2.28149.86525.10365.3149-0.1951-0.5787-0.07670.5820.09050.15090.23040.02820.10450.1324-0.042-0.0740.11290.0010.100571.70253.8321.636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 107
2X-RAY DIFFRACTION2A108 - 335
3X-RAY DIFFRACTION3A336 - 403
4X-RAY DIFFRACTION4B10 - 107
5X-RAY DIFFRACTION5B108 - 335
6X-RAY DIFFRACTION6B336 - 401

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