4D0S | pdb_00004d0s

Mtb InhA complex with Pyradizinone compound 14

PDB DOI: https://doi.org/10.2210/pdb4D0S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-04-29 Released: 2015-05-20
Deposition Author(s): Read, J.A., Breed, J., Madhavapeddi, P., Lange, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.191 (Depositor), 0.195 (DCC)
R-Value Work:
0.170 (Depositor), 0.174 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Pyridazinones: A Novel Scaffold with Excellent Physicochemical Properties and Safety Profile for a Clinically Validated Target of Mycobacterium Tuberculosis

Lange, S.

To be published.

Macromolecule Content

Total Structure Weight: 118.57 kDa
Atom Count: 8,580
Modeled Residue Count: 1,022
Deposited Residue Count: 1,076
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	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
9G4 Query on 9G4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], I [auth B], K [auth C], M [auth D]	1-{4-[(acetylamino)methyl]phenyl}-4-(4-chlorophenoxy)-6-oxo-1,6-dihydropyridazine-3-carboxamide C₂₀ H₁₇ Cl N₄ O₄ SYAJIRKWQQECEF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth D]	G [auth A], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.191 (Depositor), 0.195 (DCC)
R-Value Work: 0.170 (Depositor), 0.174 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.916	α = 90
b = 111.421	β = 98.46
c = 67.663	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2017-09-13
Changes: Data collection
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

4D0S | pdb_00004d0s

Mtb InhA complex with Pyradizinone compound 14

Literature

Pyridazinones: A Novel Scaffold with Excellent Physicochemical Properties and Safety Profile for a Clinically Validated Target of Mycobacterium Tuberculosis

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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