3K9X

X-ray crystal structure of human fxa in complex with (S)-N-((2-METHYLBENZOFURAN-5-YLAMINO)(2-OXO-1-(2-OXO-2- (PYRROLIDIN-1-YL)ETHYL)AZEPAN-3- YLAMINO)METHYLENE)NICOTINAMIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Aroylguanidine-based factor Xa inhibitors: the discovery of BMS-344577

Shi, Y., Li, C., O'Connor, S.P., Zhang, J., Shi, M., Bisaha, S.N., Wang, Y., Sitkoff, D., Pudzianowski, A.T., Huang, C., Klei, H.E., Kish, K., Yanchunas, J., Liu, E.C., Hartl, K.S., Seiler, S.M., Steinbacher, T.E., Schumacher, W.A., Atwal, K.S., Stein, P.D.

(2009) Bioorg Med Chem Lett 19: 6882-6889

  • DOI: 10.1016/j.bmcl.2009.10.084
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • We report the design and synthesis of a novel class of N,N'-disubstituted aroylguanidine-based lactam derivatives as potent and orally active FXa inhibitors. The structure-activity relationships (SAR) investigation led to the discovery of the nicotin ...

    We report the design and synthesis of a novel class of N,N'-disubstituted aroylguanidine-based lactam derivatives as potent and orally active FXa inhibitors. The structure-activity relationships (SAR) investigation led to the discovery of the nicotinoyl guanidine 22 as a potent FXa inhibitor (FXa IC(50)=4 nM, EC(2xPT)=7 microM). However, the potent CYP3A4 inhibition activity (IC(50)=0.3 microM) of 22 precluded its further development. Detailed analysis of the X-ray crystal structure of compound 22 bound to FXa indicated that the substituent at the 6-position of the nicotinoyl group of 22 would be solvent-exposed, suggesting that efforts to attenuate the unwanted CYP activity could focus at this position without affecting FXa potency significantly. Further SAR studies on the 6-substituted nicotinoyl guanidines resulted in the discovery of 6-(dimethylcarbamoyl) nicotinoyl guanidine 36 (BMS-344577, IC(50)=9 nM, EC(2xPT)=2.5 microM), which was found to be a selective, orally efficacious FXa inhibitor with an excellent in vitro liability profile, favorable pharmacokinetics and pharmacodynamics in animal models.

    Organizational Affiliation: 

    Research and Development, Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543-5400, USA. yan.shi@bms.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (Coagulation factor X)
A, C
94Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
GTEx  ENSG00000126218

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (Coagulation factor X)
B, D
238Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
GTEx  ENSG00000126218
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBM
Query on MBM
Download CCD File 
B, D
N-{N'-(2-methyl-1-benzofuran-5-yl)-N-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]carbamimidoyl}pyridine-3-carboxamide
C28 H32 N6 O4
GNYXHJVKEWBHAI-QHCPKHFHSA-N		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
A, B, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download CCD File 
B, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MBMIC50:  4   nM  BindingDB
MBMIC50:  4   nM  PDBBind
MBMIC50:  4   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.263α = 90
b = 77.63β = 102.63
c = 73.732γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description