2VWM Blood Clotting date Jun 26, 2008
title Aminopyrrolidine Factor Xa Inhibitor
authors K.Groebke-Zbinden, D.W.Banner, J.M.Benz, F.Blasco, G.Decoret, J.Himber, B.Kuhn, N.Panday, F.Ricklin, P.Risch, D.Schlatter, M.Stahl, R.Unger, W.Haap
compound source
Molecule: Activated Factor Xa Heavy Chain
Chain: A, B
Fragment: Peptidase S1 Domain, Residues 235-475
Ec: 3.4.21.6
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Factor X Light Chain
Chain: K, L
Fragment: Egf2, Residues 126-180
Ec: 3.4.21.6
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.930 77.110 74.870 90.00 92.07 90.00
method X-Ray Diffractionresolution 1.96 Å
ligand LZI, NA BindingDB enzyme Hydrolase E.C.3.4.21.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDesign of novel aminopyrrolidine factor Xa inhibitors from a screening hit., Zbinden KG, Anselm L, Banner DW, Benz J, Blasco F, Decoret G, Himber J, Kuhn B, Panday N, Ricklin F, Risch P, Schlatter D, Stahl M, Thomi S, Unger R, Haap W, Eur J Med Chem. 2009 Jul;44(7):2787-95. Epub 2009 Jan 3. PMID:19200624
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (2vwm.pdb1.gz) 55 Kb
  • Biological Unit Coordinates (2vwm.pdb2.gz) 53 Kb
  • Biological Unit Coordinates (2vwm.pdb3.gz) 46 Kb
  • Biological Unit Coordinates (2vwm.pdb4.gz) 12 Kb
  • Biological Unit Coordinates (2vwm.pdb5.gz) 44 Kb
  • Biological Unit Coordinates (2vwm.pdb6.gz) 12 Kb
  • LPC: Ligand-Protein Contacts for 2VWM
  • CSU: Contacts of Structural Units for 2VWM
  • Likely Quarternary Molecular Structure file(s) for 2VWM
  • Structure Factors (830 Kb)
  • Retrieve 2VWM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VWM from S2C, [Save to disk]
  • Re-refined 2vwm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VWM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2VWM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VWM, from MSDmotif at EBI
  • Fold representative 2vwm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vwm_A] [2vwm_B] [2vwm] [2vwm_L] [2vwm_K]
  • SWISS-PROT database: [P00742]
  • Domain organization of [FA10_HUMAN] by SWISSPFAM
  • Domains found in 2VWM: [EGF] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 2VWM with the sequences similar proteins can be viewed for 2VWM's classification [FA10_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FA10_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VWM
  • Community annotation for 2VWM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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