7UMW

Crystal structure of E. Coli FabI in complex with NAD and Fabimycin ((S,E)-3-(7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide)

PDB DOI: https://doi.org/10.2210/pdb7UMW/pdb

Classification: ANTIBIOTIC
Organism(s): Escherichia coli str. K-12 substr. MG1655
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-08 Released: 2022-12-14
Deposition Author(s): Hajian, B.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.245
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections

Parker, E.N., Cain, B.N., Hajian, B., Ulrich, R.J., Geddes, E.J., Barkho, S., Lee, H.Y., Williams, J.D., Raynor, M., Caridha, D., Zaino, A., Rohde, J.M., Zak, M., Shekhar, M., Munoz, K.A., Rzasa, K.M., Temple, E.R., Hunt, D., Jin, X., Vuong, C., Pannone, K., Kelly, A.M., Mulligan, M.P., Lee, K.K., Lau, G.W., Hung, D.T., Hergenrother, P.J.

(2022) ACS Cent Sci 8: 1362-1362

PubMed: 36188352 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acscentsci.2c00969
Primary Citation of Related Structures:
7UM8, 7UMW, 7UMX, 7UMY

PubMed Abstract:
[This corrects the article DOI: 10.1021/acscentsci.2c00598.].

Organizational Affiliation

Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

Macromolecule Content

Total Structure Weight: 58.66 kDa
Atom Count: 4,344
Modelled Residue Count: 519
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI	A, B	266	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: fabI EC: 1.3.1.9
UniProt
Find proteins for P0AEK4 (Escherichia coli (strain K12)) Explore P0AEK4 Go to UniProtKB: P0AEK4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEK4
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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NUC (Subject of Investigation/LOI) Query on NUC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	(2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide C₂₃ H₂₄ N₄ O₃ ZWQNEFFHBSGFHV-HKMNZKMDSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]