4ELB

Structure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase

PDB DOI: https://doi.org/10.2210/pdb4ELB/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Bacillus anthracis str. Sterne
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-04-10 Released: 2013-02-13
Deposition Author(s): Bourne, C.R., Barrow, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.309
R-Value Work: 0.243
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase.

Bourne, C.R., Wakeham, N., Nammalwar, B., Tseitin, V., Bourne, P.C., Barrow, E.W., Mylvaganam, S., Ramnarayan, K., Bunce, R.A., Berlin, K.D., Barrow, W.W.

(2013) Biochim Biophys Acta 1834: 46-52

PubMed: 22999981 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bbapap.2012.09.001
Primary Citation of Related Structures:
4ELB, 4ELE, 4ELF, 4ELG, 4ELH

PubMed Abstract:
Bacterial resistance to antibiotic therapies is increasing and new treatment options are badly needed. There is an overlap between these resistant bacteria and organisms classified as likely bioterror weapons. For example, Bacillus anthracis is innately resistant to the anti-folate trimethoprim due to sequence changes found in the dihydrofolate reductase enzyme. Development of new inhibitors provides an opportunity to enhance the current arsenal of anti-folate antibiotics while also expanding the coverage of the anti-folate class.

Organizational Affiliation

Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA. christina.bourne@okstate.edu

Macromolecule Content

Total Structure Weight: 162.73 kDa
Atom Count: 12,054
Modelled Residue Count: 1,328
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A B [auth H] C D [auth B] E [auth G] A, B [auth H], C, D [auth B], E [auth G], F, G [auth D], H [auth E]	166	Bacillus anthracis str. Sterne	Mutation(s): 0 Gene Names: BAS2083, BA_2237, dfrA, DHFR, GBAA_2237 EC: 1.5.1.3
UniProt
Find proteins for Q81R22 (Bacillus anthracis) Explore Q81R22 Go to UniProtKB: Q81R22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q81R22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
34R Query on 34R Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain Q [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain Q [auth C]	AA [auth F], DA [auth D], HA [auth E], Q [auth C]	(2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1R)-1-phenylphthalazin-2(1H)-yl]prop-2-en-1-one C₃₀ H₂₈ N₆ O₃ NFQBNKYRVDDBSW-DBQZHCBRSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain Q [auth C] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain Q [auth C]
34S Query on 34S Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain T [auth B] SDF format, chain W [auth G] SDF format, chain Z [auth F] SDF format, chain K [auth A] SDF format, chain M [auth H] MOL2 format, chain GA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain K [auth A] MOL2 format, chain M [auth H]	GA [auth E] K [auth A] M [auth H] T [auth B] W [auth G] GA [auth E], K [auth A], M [auth H], T [auth B], W [auth G], Z [auth F]	(2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-phenylphthalazin-2(1H)-yl]prop-2-en-1-one C₃₀ H₂₈ N₆ O₃ NFQBNKYRVDDBSW-QSRYBZNWSA-N		Interactions Focus chain GA [auth E] Focus chain K [auth A] Focus chain M [auth H] Focus chain T [auth B] Focus chain W [auth G] Focus chain Z [auth F] Interactions & Density Focus chain GA [auth E] Focus chain K [auth A] Focus chain M [auth H] Focus chain T [auth B] Focus chain W [auth G] Focus chain Z [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain L [auth H] SDF format, chain R [auth B] SDF format, chain U [auth G] SDF format, chain X [auth F] SDF format, chain EA [auth E] SDF format, chain I [auth A] SDF format, chain O [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain L [auth H] MOL2 format, chain R [auth B] MOL2 format, chain U [auth G] MOL2 format, chain X [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C]	BA [auth D] EA [auth E] I [auth A] L [auth H] O [auth C] BA [auth D], EA [auth E], I [auth A], L [auth H], O [auth C], R [auth B], U [auth G], X [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain I [auth A] Focus chain L [auth H] Focus chain O [auth C] Focus chain R [auth B] Focus chain U [auth G] Focus chain X [auth F] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain I [auth A] Focus chain L [auth H] Focus chain O [auth C] Focus chain R [auth B] Focus chain U [auth G] Focus chain X [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain J [auth A] SDF format, chain N [auth H] SDF format, chain P [auth C] SDF format, chain S [auth B] SDF format, chain V [auth G] SDF format, chain Y [auth F] SDF format, chain CA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain N [auth H] MOL2 format, chain P [auth C] MOL2 format, chain S [auth B] MOL2 format, chain V [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain CA [auth D]	CA [auth D] FA [auth E] J [auth A] N [auth H] P [auth C] CA [auth D], FA [auth E], J [auth A], N [auth H], P [auth C], S [auth B], V [auth G], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain FA [auth E] Focus chain J [auth A] Focus chain N [auth H] Focus chain P [auth C] Focus chain S [auth B] Focus chain V [auth G] Focus chain Y [auth F] Interactions & Density Focus chain CA [auth D] Focus chain FA [auth E] Focus chain J [auth A] Focus chain N [auth H] Focus chain P [auth C] Focus chain S [auth B] Focus chain V [auth G] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.309
R-Value Work: 0.243
R-Value Observed: 0.247
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.874	α = 90
b = 135.444	β = 90
c = 168.194	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Bourne, C.R.

Barrow, W.W.

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4ELB

Structure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase

Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)