7UMX | pdb_00007umx

Crystal structure of Acinetobacter baumannii FabI in complex with NAD and (R,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/pdb7UMX/pdb

Classification: ANTIBIOTIC
Organism(s): Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-08 Released: 2023-02-15
Deposition Author(s): Hajian, B.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.251 (Depositor), 0.363 (DCC)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acscentsci.2c00969
Primary Citation 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: 180.58 kDa
Atom Count: 12,224
Modeled Residue Count: 1,558
Deposited Residue Count: 1,626
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	271	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0 Gene Names: fabI EC: 1.3.1.9
UniProt
Find proteins for D0CAD5 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CAD5 Go to UniProtKB: D0CAD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0CAD5
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 H [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F] mmCIF format, chain J [auth B]	H [auth A] J [auth B] K [auth C] N [auth D] O [auth E] H [auth A], J [auth B], K [auth C], N [auth D], O [auth E], R [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain R [auth F]
NQF (Subject of Investigation/LOI) Query on NQF Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	G [auth A] I [auth B] L [auth C] M [auth D] P [auth E] G [auth A], I [auth B], L [auth C], M [auth D], P [auth E], Q [auth F]	(2E)-3-[(7R)-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-RUJXFNLJSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain Q [auth F]