[English] 日本語
Yorodumi
- PDB-28iv: structure of InhA from Mycobacterium tuberculosis in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 28iv
Titlestructure of InhA from Mycobacterium tuberculosis in complex with (E)-2-(4-(4-((4-cyclopropyl-1H-1,2,3-triazol-1-yl)methyl)-2-hydroxyphenoxy)-3-chlorobenzylidene)hydrazine-1-carbothioamide (compound 6d)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / ENOYL-ACP-REDUCTASE TYPE II FATTY ACID SYNTHASE MYCOLIC ACIDS TUBERCULOSIS THERAPEUTIC TARGET OXIDOREDUCTASE
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.958 Å
AuthorsTamhaev, R. / Lherbet, C. / Azema-Despeyroux, J. / Mourey, L. / Maveyraud, L.
Funding support France, Italy, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE44-0002 France
Universite de Toulouse France
La Region Occitanie Italy
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: J.Med.Chem. / Year: 2026
Title: Rational Design of Diaryl Ether-Based Dual Inhibitors Targeting Successive Essential Enzymes HadAB and InhA in Mycobacterium tuberculosis.
Authors: Tamhaev, R. / Recchia, D. / Zahorszka, M. / Stelitano, G. / Chiarelli, L.R. / Rizet, J. / Rima, J. / Chebaiki, M. / Valentin, L. / Azema-Despeyroux, J. / Hoffmann, P. / Preuilh, N. / Dumais, ...Authors: Tamhaev, R. / Recchia, D. / Zahorszka, M. / Stelitano, G. / Chiarelli, L.R. / Rizet, J. / Rima, J. / Chebaiki, M. / Valentin, L. / Azema-Despeyroux, J. / Hoffmann, P. / Preuilh, N. / Dumais, B. / Britton, S. / Degiacomi, G. / Maveyraud, L. / Kordulakova, J. / Pasca, M.R. / Mourey, L. / Lherbet, C.
History
DepositionFeb 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,07613
Polymers115,3484
Non-polymers4,7289
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19140 Å2
ΔGint-132 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.73, 92.13, 103.98
Angle α, β, γ (deg.)90, 107.43, 90
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / ENR / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28837.057 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MTCY277.05 / Plasmid: pET15b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-A1JY6 / (E)-2-(4-(4-((4-cyclopropyl-1H-1,2,3-triazol-1-yl)methyl)-2-hydroxyphenoxy)-3-chlorobenzylidene)hydrazine-1-carbothioamide / 1-[({E})-[3-chloranyl-4-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]phenyl]methylideneamino]thiourea


Mass: 442.922 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H19ClN6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: PEG 4000 14 % (w/v) ADA buffer 0.1 M Ammonium Acetate 0.1 M DMSO 5 % (v/v) NAD+ 2.8 mM, Compound 2.5 mM

-
Data collection

DiffractionMean temperature: 121 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.958→99.207 Å / Num. obs: 80986 / % possible obs: 99.4 % / Redundancy: 6.95 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.998 / CC1/2 anomalous: -0.278 / Rmerge(I) obs: 0.0897 / Rpim(I) all: 0.0368 / Rrim(I) all: 0.0971 / AbsDiff over sigma anomalous: 0.765 / Net I/σ(I): 13.06 / Num. measured all: 563012 / % possible anomalous: 99.4 / Redundancy anomalous: 3.53
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
5.313-99.2076.660.040535.132763127631415141510.999-0.370.01690.0440.62799.83.4899.1
4.217-5.3136.890.045834.12795027950405840580.998-0.3620.01870.04960.6599.23.5399
3.684-4.2176.340.049930.322572725727405540550.997-0.3230.02140.05440.70798.43.2598.7
3.347-3.6846.620.0627.032678426784404540450.997-0.30.02520.06510.74698.53.3898.8
3.107-3.3476.140.075621.712475224752403140310.995-0.1990.03330.08280.80798.93.1398.7
2.924-3.1076.730.099418.442735627356406340630.994-0.1530.04140.10780.82999.43.4299.6
2.778-2.9246.950.120415.852786927869401240120.993-0.120.04910.13010.80299.63.5399.8
2.657-2.7787.090.161512.862906329063410041000.99-0.0960.06520.17430.80499.73.5999.7
2.555-2.6577.220.200811.042933229332406540650.984-0.0650.08030.21640.80699.63.6599.7
2.466-2.5557.240.25439.122927329273404440440.976-0.030.10130.2740.79599.73.6799.7
2.389-2.4667.260.28338.142958729587407440740.978-0.050.11250.3050.78399.73.6899.7
2.321-2.3897.310.33737.132934229342401540150.968-0.0350.13350.3630.79999.83.6999.8
2.26-2.3217.340.39256.082985229852406640660.9590.010.15470.42220.80199.63.7199.6
2.205-2.267.340.49165.172955029550402640260.936-0.0280.19390.52880.78199.63.7199.6
2.155-2.2057.360.52554.672982729827405540550.92-0.0210.20680.56510.76599.53.7299.4
2.109-2.1557.260.65883.72893828938398839880.894-0.0210.26150.70940.7599.73.6799.7
2.067-2.1096.620.766232706827068408740870.789-0.0230.32190.83250.76899.93.3699.9
2.028-2.0676.670.86432.582715827158407040700.763-0.0360.36160.93830.76199.43.3899.4
1.991-2.0286.960.99922.262784527845400240020.725-0.0330.40721.07990.75999.23.5299.2
1.958-1.9917.061.151.932810828108397939790.694-0.0320.46381.24090.76299.23.5699.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data processing
XSCALEdata scaling
TRUNCATE9.0.005data processing
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENY

1eny


Resolution: 1.958→99.207 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 4056 -RANDOM
Rwork0.1757 76927 --
obs0.1768 80983 99.4 %-
Displacement parametersBiso mean: 42.23 Å2
Baniso -1Baniso -2Baniso -3
1-4.4807 Å20 Å24.7582 Å2
2---1.9543 Å20 Å2
3----2.5264 Å2
Refine analyzeLuzzati coordinate error obs: 0.213 Å
Refinement stepCycle: LAST / Resolution: 1.958→99.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7829 0 314 575 8718
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088389HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9211445HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2863SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1481HARMONIC5
X-RAY DIFFRACTIONt_it8389HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1119SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact7856SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 1.96→1.97 Å
RfactorNum. reflection% reflection
Rfree0.2701 83 -
Rwork0.2708 1537 -
obs0.2708 1620 98.97 %
Refinement TLS params.

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)
11.3384-0.25660.05151.28360.02580.77450.0252-0.0151-0.3147-0.1066-0.00990.09940.10780.1217-0.0152-0.04160.0746-0.0339-0.08320.00480.016930.70150.34619.7244
21.6241-0.5837-0.14821.8440.12620.68780.0641-0.0747-0.1945-0.059-0.03780.3966-0.1171-0.1091-0.0263-0.07510.0608-0.0397-0.08090.00510.04185.243120.591923.2282
31.5233-0.07080.13661.0206-0.17880.90820.04140.03020.3949-0.0571-0.0078-0.0315-0.31690.0975-0.03360.0774-0.00310.0067-0.14680.00230.029425.882643.563415.7312
41.3581-0.17730.17971.1469-0.2171.1456-0.024-0.20750.13630.1161-0.0073-0.2301-0.15990.36990.0312-0.0798-0.0363-0.04630.0755-0.0192-0.053548.162524.757730.9514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 269
2X-RAY DIFFRACTION1{ A|* }A301 - 302
3X-RAY DIFFRACTION2{ B|* }B2 - 269
4X-RAY DIFFRACTION2{ B|* }B301 - 302
5X-RAY DIFFRACTION3{ C|* }C2 - 269
6X-RAY DIFFRACTION3{ C|* }C301 - 302
7X-RAY DIFFRACTION4{ D|* }D3 - 269
8X-RAY DIFFRACTION4{ D|* }D301 - 303

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more