4UVH | pdb_00004uvh

Discovery of pyrimidine isoxazoles InhA in complex with compound 10

PDB DOI: https://doi.org/10.2210/pdb4UVH/pdb

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

Deposited: 2014-08-05 Released: 2015-09-30
Deposition Author(s): Read, J.A., Gingell, H., Madhavapeddi, P., Ghorpade, S., Cowan, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.186 (Depositor), 0.192 (DCC)
R-Value Work:
0.153 (Depositor), 0.161 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Hitting the Target in More Than One Way: Novel, Direct Inhibitors of Mycobacterium Tuberculosis Enoyl Acp Reductase

Madhavapeddi, P., Kale, R.R., Cowen, S.D., Ghorpade, S.R., Davies, G., Bellale, E.V., Kale, M.G., Srivastava, A., Spadola, L., Kawatkar, A., Raichurkar, A.V., Tonge, M., Nandishaiah, R., Guptha, S., Narayan, A., Gingell, H., Plant, D., Landge, S., Menasinakai, S., Prabhakar, K.R., Achar, V., Ambady, A., Sambandamurthy, V.K., Ramachandran, V., Panduga, V., Reddy, J., Kumar, C.N.N., Kaur, P., Shandil, R., Iyer, P.S., Narayanan, S., Read, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 117.76 kDa
Atom Count: 8,421
Modeled Residue Count: 1,023
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 M [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], M [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 K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
UUD Query on UUD Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], N [auth D]	N-(1,3-BENZOTHIAZOL-2-YL)ACETAMIDE C₉ H₈ N₂ O S RIYZWBJLPINWTC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.186 (Depositor), 0.192 (DCC)
R-Value Work: 0.153 (Depositor), 0.161 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.817	α = 90
b = 111.032	β = 98.58
c = 67.665	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-30
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other