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)


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 1.2 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D, E
A, B, C, D, E, F
271Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0CAD5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
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
NUC (Subject of Investigation/LOI)
Query on NUC

Download Ideal Coordinates CCD File 
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
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 = 256.215α = 90
b = 79.137β = 110.297
c = 89.425γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-02-15 
  • Deposition Author(s): Hajian, B.

Funding OrganizationLocationGrant Number
Other privateUnited 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