7UMY

Crystal structure of Acinetobacter baumannii 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/pdb7UMY/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: 2.74 Å
R-Value Free: 0.296
R-Value Work: 0.256
R-Value Observed: 0.260

Starting Model: experimental
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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: 180.58 kDa
Atom Count: 11,921
Modelled Residue Count: 1,551
Deposited Residue Count: 1,626
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]	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 L [auth C] SDF format, chain M [auth D] SDF format, chain P [auth E] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain R [auth F] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain P [auth E] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth F] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain P [auth E] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth F]	G [auth A] J [auth B] L [auth C] M [auth D] P [auth E] G [auth A], J [auth B], L [auth C], M [auth D], P [auth E], R [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain R [auth F]
NUC (Subject of Investigation/LOI) Query on NUC Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E]	H [auth A] I [auth B] K [auth C] N [auth D] O [auth E] H [auth A], I [auth B], K [auth C], N [auth D], O [auth E], Q [auth F]	(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 H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.296
R-Value Work: 0.256
R-Value Observed: 0.260
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 256.215	α = 90
b = 79.137	β = 110.297
c = 89.425	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
Coot	model building
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Hajian, B.

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2023-08-16
Changes: Data collection, Source and taxonomy
Version 1.2: 2023-10-25
Changes: Refinement description
Version 1.3: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary

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Help and Resources

7UMY

Crystal structure of Acinetobacter baumannii 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)

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

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)