Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 32.75 kDa 
• Atom Count: 2503 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

2BMG

Crystal structure of factor Xa in complex with 50

• PDB DOI: 10.2210/pdb2BMG/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-03-14 Released: 2006-03-08 
• Deposition Author(s): Schreuder, H., Matter, H., Will, D.W., Nazare, M., Laux, V., Wehner, V., Loenze, P., Liesum, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.193 

Literature

Structural Requirements for Factor Xa Inhibition by 3-Oxybenzamides with Neutral P1 Substituents: Combining X-Ray Crystallography, 3D-Qsar and Tailored Scoring Functions

Matter, H., Will, D.W., Nazare, M., Schreuder, H., Laux, V., Wehner, V., Liesum, A.

(2005) J Med Chem 48: 3290

• PubMed: 15857135 
• DOI: 10.1021/jm049187l
• Primary Citation of Related Structures:  
  2BMG


• PubMed Abstract: 
  

The design, synthesis, and structure-activity relationship of 3-oxybenzamides as potent inhibitors of the coagulation protease factor Xa are described on the basis of X-ray structures, privileged structure motifs, and SAR information. A total of six X-ray structures of fXa/inhibitor complexes led us to identify the major protein-ligand interactions. The binding mode is characterized by a lipophilic dichlorophenyl substituent interacting with Tyr228 in the protease S1 pocket, while polar parts are accommodated in S4. This alignment in combination with docking allowed derivation of 3D-QSAR models and tailored scoring functions to rationalize biological affinity and provide guidelines for optimization. The resulting models showed good correlation coefficients and predictions of external test sets. Furthermore, they correspond to binding site topologies in terms of steric, electrostatic, and hydrophobic complementarity. Two approaches to derive tailored scoring functions combining binding site and ligand information led to predictive models with acceptable predictions of the external set. Good correlations to experimental affinities were obtained for both AFMoC (adaptation of fields for molecular comparison) and the novel TScore function. The SAR information from 3D-QSAR and tailored scoring functions agrees with all experimental data and provides guidelines and reasonable activity estimations for novel fXa inhibitors.

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Organizational Affiliation: 

DI and A Chemistry, Aventis Pharma Deutschland GmbH, A Company of the Sanofi-Aventis Group, Building G 878, D-65926 Frankfurt am Main, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	A	53	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	B	234	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I1H	D [auth B]	3-[2-(2,4-DICHLOROPHENYL)ETHOXY]-4-METHOXY-N-[(1-PYRIDIN-4-YLPIPERIDIN-4-YL)METHYL]BENZAMIDE C27 H29 Cl2 N3 O3 UVSAHJWEJXWVGO-UHFFFAOYSA-N
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I1H	PDBBind:  2BMG	Ki: 18 (nM) from 1 assay(s)
	BindingDB:  2BMG	Ki: 18 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57	α = 90
b = 72.3	β = 90
c = 78.1	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
XDS	data reduction
XSCALE	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-14 
• Released Date: 2006-03-08 
Deposition Author(s): Schreuder, H., Matter, H., Will, D.W., Nazare, M., Laux, V., Wehner, V., Loenze, P., Liesum, A.

Revision History  

• Version 1.0: 2006-03-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2019-01-30
  Changes: Data collection, Experimental preparation