2B37 | pdb_00002b37

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

PDB DOI: https://doi.org/10.2210/pdb2B37/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: 2.60 Å
R-Value Free:
0.294 (Depositor), 0.299 (DCC)
R-Value Work:
0.225 (Depositor), 0.231 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 175.91 kDa
Atom Count: 11,736
Modeled Residue Count: 1,521
Deposited Residue Count: 1,614
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] J [auth C] L [auth D] M [auth E] G [auth A], H [auth B], J [auth C], L [auth D], M [auth E], N [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F]
8PS Query on 8PS Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	I [auth C], K [auth D]	5-OCTYL-2-PHENOXYPHENOL C₂₀ H₂₆ O₂ JOWYBLIPWAMIHM-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
8PS	BindingDB: 2B37	Ki: min: 1, max: 1.1 (nM) from 2 assay(s)
8PS	BindingDB: 2B37	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.294 (Depositor), 0.299 (DCC)
R-Value Work: 0.225 (Depositor), 0.231 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.341	α = 90
b = 100.293	β = 90
c = 379.275	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

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: 2024-02-14
Changes: Data collection, Database references, Derived calculations

2B37 | pdb_00002b37

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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