2B36

Crystal structure of Mycobacterium tuberculosis enoyl reductase (InhA) inhibited by 5-pentyl-2-phenoxyphenol

PDB DOI: https://doi.org/10.2210/pdb2B36/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-09-19 Released: 2006-03-07
Deposition Author(s): Sullivan, T.J., Truglio, J.J., Novichenok, P., Stratton, C., Zhang, X., Kaur, T., Johnson, F., Boyne, M.S., Amin, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.295
R-Value Work: 0.242
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

High Affinity InhA Inhibitors with Activity against Drug-Resistant Strains of Mycobacterium tuberculosis

Sullivan, T.J., Truglio, J.J., Boyne, M.E., Novichenok, P., Zhang, X., Stratton, C., Li, H.J., Kaur, T., Amin, A., Johnson, F., Slayden, R.A., Kisker, C., Tonge, P.J.

(2006) ACS Chem Biol 1: 43-53

Macromolecule Content

Total Structure Weight: 176.85 kDa
Atom Count: 11,841
Modelled Residue Count: 1,528
Deposited Residue Count: 1,614
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D, E A, B, C, D, E, F	269	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: inhA EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGR1 Go to UniProtKB: P9WGR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
5PP Query on 5PP Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain G [auth A] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	5-PENTYL-2-PHENOXYPHENOL C₁₇ H₂₀ O₂ OJLYTHOKCYLPMA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Binding Affinity Annotations
ID	Source	Binding Affinity
5PP	BindingDB: 2B36	Ki: 11.8 (nM) from 1 assay(s)
5PP	BindingDB: 2B36	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.295
R-Value Work: 0.242
R-Value Observed: 0.245
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.955	α = 90
b = 81.827	β = 95.69
c = 188.656	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-07
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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Help and Resources

2B36

Crystal structure of Mycobacterium tuberculosis enoyl reductase (InhA) inhibited by 5-pentyl-2-phenoxyphenol

High Affinity InhA Inhibitors with Activity against Drug-Resistant Strains of Mycobacterium tuberculosis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)