Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34283.89 
• Atom Count: 2271 
• 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


• 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: 2.2 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:  
  2BQW, 2BQ6, 2BOH


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
COAGULATION FACTOR X	A	52	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Go to Gene View: F10 Go to UniProtKB:  P00742

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
FACTOR XA	B	249	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Go to Gene View: F10 Go to UniProtKB:  P00742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IID	A	N-(1-ISOPROPYLPIPERIDIN-4-YL)-1-(3-METHOXYBENZYL)-1H-INDOLE-2-CARBOXAMIDE 1-(3-METHOXY-BENZYL)-1H-INDOLE-2-CARBOXYLIC ACID (1-ISOPROPYL-PIPERIDIN- 4-YL)-AMIDE C25 H31 N3 O2 GIPCBGDQVGKMPO-UHFFFAOYSA-N
CA	B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IID	Ki: 89 nM (100) BINDINGDB
IID	Ki: 89 nM BINDINGMOAD
IID	Ki: 89 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 55.940	α = 90.00
b = 72.050	β = 90.00
c = 78.550	γ = 90.00

Software Package:

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

Structure Validation

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-01-30
  Type: Data collection, Experimental preparation, Other