2VVC

Aminopyrrolidine Factor Xa inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2VVC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-06-05 Released: 2009-07-07 
• Deposition Author(s): Groebke-Zbinden, K., Banner, D.W., Benz, J.M., Blasco, F., Decoret, G., Himber, J., Kuhn, B., Panday, N., Ricklin, F., Risch, P., Schlatter, D., Stahl, M., Unger, R., Haap, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.275 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit.

Zbinden, K.G., Anselm, L., Banner, D.W., Benz, J.M., Blasco, F., Decoret, G., Himber, J., Kuhn, B., Panday, N., Ricklin, F., Risch, P., Schlatter, D., Stahl, M., Thomi, S., Unger, R., Haap, W.

(2009) Eur J Med Chem 44: 2787

• PubMed: 19200624 
• DOI: https://doi.org/10.1016/j.ejmech.2008.12.025
• Primary Citation of Related Structures:  
  2VVC, 2VVU, 2VVV, 2VWL, 2VWM, 2VWN, 2VWO


• PubMed Abstract: 
  

  Starting from a hit identified by focused screening, 3-aminopyrrolidine factor Xa inhibitors were designed. The binding mode as determined by X-ray structural analysis as well as the pharmacokinetic behaviour of selected compounds is discussed.

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Organizational Affiliation: 

F Hoffmann - La Roche Ltd, Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.56 kDa 
• Atom Count: 5,086 
• Modelled Residue Count: 564 
• Deposited Residue Count: 592 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	A, B	241	Homo sapiens	Mutation(s): 1  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X LIGHT CHAIN	C [auth K], D [auth L]	55	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
GTEx:  ENSG00000126218

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LZF	E [auth A], H [auth B]	5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide C23 H22 Cl F N4 O4 S BOCLXHFYRGMFSC-ROUUACIJSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	G [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LZF	PDBBind:  2VVC	Ki: 3 (nM) from 1 assay(s)
	BindingDB:  2VVC	Ki: min: 3, max: 3000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.275 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.96	α = 90
b = 77.19	β = 92.12
c = 74.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Groebke-Zbinden, K., Banner, D.W., Benz, J.M., Blasco, F., Decoret, G., Himber, J., Kuhn, B., Panday, N., Ricklin, F., Risch, P., Schlatter, D., Stahl, M., Unger, R., Haap, W.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description