Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 34.28 kDa 
• Atom Count: 2561 
• Modelled Residue Count: 286 
• Deposited Residue Count: 301 
• Unique protein chains: 2

2BQ7

Crystal structure of factor Xa in complex with 43

• DOI: 10.2210/pdb2BQ7/pdb

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


• Deposited: 2005-04-27 Released: 2006-04-26 
• Deposition Author(s): Nazare, M., Will, D.W., Matter, H., Schreuder, H., Ritter, K., Urmann, M., Essrich, M., Bauer, A., Wagner, M., Czech, J., Laux, V., Wehner, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 

Literature

Probing the Subpockets of Factor Xa Reveals Two Binding Modes for Inhibitors Based on a 2-Carboxyindole Scaffold: A Study Combining Structure-Activity Relationship and X-Ray Crystallography.

Nazare, M., Will, D.W., Matter, H., Schreuder, H., Ritter, K., Urmann, M., Essrich, M., Bauer, A., Wagner, M., Czech, J., Lorenz, M., Laux, V., Wehner, V.

(2005) J Med Chem 48: 4511

• PubMed: 15999990 
• DOI: 10.1021/jm0490540
• Primary Citation of Related Structures:  
  2BOH, 2BQ6, 2BQ7, 2BQW


• PubMed Abstract: 
  

Structure-activity relationships within a series of highly potent 2-carboxyindole-based factor Xa inhibitors incorporating a neutral P1 ligand are described with particular emphasis on the structural requirements for addressing subpockets of the factor Xa enzyme. Interactions with the subpockets were probed by systematic substitution of the 2-carboxyindole scaffold, in combination with privileged P1 and P4 substituents. Combining the most favorable substituents at the indole nucleus led to the discovery of a remarkably potent factor Xa inhibitor displaying a K(i) value of 0.07 nM. X-ray crystallography of inhibitors bound to factor Xa revealed substituent-dependent switching of the inhibitor binding mode and provided a rationale for the SAR obtained. These results underscore the key role played by the P1 ligand not only in determining the binding affinity of the inhibitor by direct interaction but also in modifying the binding mode of the whole scaffold, resulting in a nonlinear SAR.

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Organizational Affiliation: 

Aventis Pharma Deutschland GmbH, a company of the Sanofi-Aventis group, Industriepark Höchst, Frankfurt am Main, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	A	52	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 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR XA	B	249	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 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IID (Subject of Investigation/LOI)	C [auth A]	N-(1-ISOPROPYLPIPERIDIN-4-YL)-1-(3-METHOXYBENZYL)-1H-INDOLE-2-CARBOXAMIDE C25 H31 N3 O2 GIPCBGDQVGKMPO-UHFFFAOYSA-N
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IID	Binding MOAD:  2BQ7	Ki: 89 (nM) from 1 assay(s)
	PDBBind:  2BQ7	Ki: 89 (nM) from 1 assay(s)
	BindingDB:  2BQ7	Ki: 89 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.94	α = 90
b = 72.05	β = 90
c = 78.55	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-04-27 
• Released Date: 2006-04-26 
Deposition Author(s): Nazare, M., Will, D.W., Matter, H., Schreuder, H., Ritter, K., Urmann, M., Essrich, M., Bauer, A., Wagner, M., Czech, J., Laux, V., Wehner, V.

Revision History  

• Version 1.0: 2006-04-26
  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: 2019-01-30
  Changes: Data collection, Experimental preparation, Other