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GeezerVison is showing www.rcsb.org — RCSB PDB - 2VWM: Aminopyrrolidine Factor Xa inhibitor

  • Structure Summary
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  • Structure Factors (CIF)
  • Structure Factors (CIF - gz)
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  • Validation (CIF - gz)
  • Validation 2fo-fc coefficients (CIF - gz)
  • Validation fo-fc coefficients (CIF - gz)
  • Biological Assembly 1 (CIF - gz) 
  • Biological Assembly 2 (CIF - gz) 
  • Biological Assembly 3 (CIF - gz) 
  • Biological Assembly 4 (CIF - gz) 
  • Biological Assembly 5 (CIF - gz) 
  • Biological Assembly 6 (CIF - gz) 
  • Biological Assembly 1 (PDB - gz)
  • Biological Assembly 2 (PDB - gz)
  • Biological Assembly 3 (PDB - gz)
  • Biological Assembly 4 (PDB - gz)
  • Biological Assembly 5 (PDB - gz)
  • Biological Assembly 6 (PDB - gz)
 Data API 

 2VWM | pdb_00002vwm

Aminopyrrolidine Factor Xa inhibitor

  • PDB DOI: https://doi.org/10.2210/pdb2VWM/pdb
  • Classification: BLOOD CLOTTING
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2008-06-26 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.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.273 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2VWM

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

  • Download Mendeley

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 Search on PubMed
  • DOI: https://doi.org/10.1016/j.ejmech.2008.12.025
  • Primary Citation 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.

    • Organizational Affiliation: 
    • F Hoffmann - La Roche Ltd, Basel, Switzerland. [email protected]
Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

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

Find Similar Assemblies

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

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

Find Similar Assemblies

Biological assembly 2 generated by PQS (software)

Biological Assembly 3  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

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

Find Similar Assemblies

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

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

Find Similar Assemblies

Biological assembly 4 assigned by authors.

Biological Assembly 5  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

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

Find Similar Assemblies

Biological assembly 5 assigned by authors.

Biological Assembly 6  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (LZI)

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

Find Similar Assemblies

Biological assembly 6 assigned by authors.

Macromolecule Content 

  • Total Structure Weight: 67.66 kDa 
  • Atom Count: 5,099 
  • Modeled Residue Count: 563 
  • Deposited Residue Count: 592 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA HEAVY CHAIN
A, B
241Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FACTOR X LIGHT CHAINC [auth K],
D [auth L]		55Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LZI

Query on LZI


Download:Ideal Coordinates CCD File
  • SDF format, chain E [auth A]
  • SDF format, chain G [auth B]
  • MOL2 format, chain E [auth A]
  • MOL2 format, chain G [auth B]
  • mmCIF format, chain E [auth A]
  • mmCIF format, chain G [auth B]
E [auth A],
G [auth B]		(4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide
C27 H27 Cl F N5 O4 S
LRFNMAKOTZSBFP-UTKZUKDTSA-N
Interactions
  • Focus chain E [auth A]
  • Focus chain G [auth B]
Interactions & Density
  • Focus chain E [auth A]
  • Focus chain G [auth B]
NA

Query on NA


Download:Ideal Coordinates CCD File
  • SDF format, chain H [auth B]
  • SDF format, chain F [auth A]
  • MOL2 format, chain H [auth B]
  • MOL2 format, chain F [auth A]
  • mmCIF format, chain H [auth B]
  • mmCIF format, chain F [auth A]
F [auth A],
H [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Interactions
  • Focus chain F [auth A]
  • Focus chain H [auth B]
Interactions & Density
  • Focus chain F [auth A]
  • Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.273 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.93α = 90
b = 77.11β = 92.07
c = 74.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

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  (Full details and data files)

  • Version 1.0: 2009-07-07
    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: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary
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