Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.23 kDa 
• Atom Count: 2608 
• Modelled Residue Count: 287 
• Deposited Residue Count: 388 
• Unique protein chains: 2

1LPK

CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 125.

• PDB DOI: 10.2210/pdb1LPK/pdb

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


• Deposited: 2002-05-08 Released: 2003-05-08 
• Deposition Author(s): Schreuder, H.A., Loenze, P., Brachvogel, V., Liesum, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.280 
• R-Value Work: 0.192 

Literature

Design and Quantitative Structure-Activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa

Matter, H., Defossa, E., Heinelt, U., Blohm, P.M., Schneider, D., Mueller, A., Herok, S., Schreuder, H.A., Liesum, A., Brachvogel, V., Loenze, P., Walser, A., Al-Obeidi, F., Wildgoose, P.

(2002) J Med Chem 45: 2749-2769

• PubMed: 12061878 
• DOI: 10.1021/jm0111346
• Primary Citation of Related Structures:  
  1LPG, 1LPK, 1LPZ, 1LQD, 1LQE


• PubMed Abstract: 
  

A series of 138 nonchiral 3-amidinobenzyl-1H-indole-2-carboxamides and analogues as inhibitors of the blood coagulation enzyme factor Xa (fXa) were designed, synthesized, and investigated by X-ray structure analysis and 3D quantitative structure-activity relationship (QSAR) studies (CoMFA, CoMSIA) in order to identify important protein-ligand interactions responsible for biological affinity and selectivity. Several compounds from this series are highly potent and selective inhibitors of this important enzyme linking extrinsic and intrinsic coagulation pathways. To rationalize biological affinity and to provide guidelines for further design, all compounds were docked into the factor Xa binding site. Those docking studies were based on X-ray structures of factor Xa in complex with literature-known inhibitors. It was possible to validate those binding modes by four X-ray crystal structures of representative ligands in factor Xa, while one ligand was additionally crystallized in trypsin to rationalize requirements for selective factor Xa inhibition. The 3D-QSAR models based on a superposition rule derived from these docking studies were validated using conventional and cross-validated r(2) values using the leave-one-out method and repeated analyses using two randomly chosen cross-validation groups plus randomization of biological activities. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which were found to correspond to experimentally determined factor Xa binding site topology in terms of steric, electrostatic, and hydrophobic complementarity. Subsets selected as smaller training sets using 2D fingerprints and maximum dissimilarity methods resulted in 3D-QSAR models with remarkable correlation coefficients and a high predictive power. The final quantitative SAR information agrees with all experimental data for the binding topology and thus provides reasonable activity predictions for novel factor Xa inhibitors.

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Organizational Affiliation: 

Aventis Pharma Deutschland GmbH, DI&A, Molecular Modeling, Building G 878, D-65926 Frankfurt am Main, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blood coagulation factor Xa	A	134	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
Blood coagulation factor Xa	B	254	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
CBB	D [auth B]	1-(3-CARBAMIMIDOYL-BENZYL)-1H-INDOLE-2-CARBOXYLIC ACID 3-CARBAMIMIDOYL-BENZYLESTER C25 H23 N5 O2 ZJZBBFMRHRUCQD-UHFFFAOYSA-N
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CBB	Binding MOAD:  1LPK	Ki: 28 (nM) from 1 assay(s)
	PDBBind:  1LPK	Ki: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.280 
• R-Value Work: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.702	α = 90
b = 72.196	β = 90
c = 78.612	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-08 
• Released Date: 2003-05-08 
Deposition Author(s): Schreuder, H.A., Loenze, P., Brachvogel, V., Liesum, A.

Revision History  

• Version 1.0: 2003-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-10-27
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary