2F9B Hydrolase Blood Clotting date Dec 05, 2005
title Discovery Of Novel Heterocyclic Factor Viia Inhibitors
authors R.Rai, A.Kolesnikov, P.A.Sprengeler, S.Torkelson, T.Ton, B.A.Katz, C.Yu, J.Hendrix, W.D.Shrader, R.Stephens, R.Cabuslay, E.Sanford, W.B.Young
compound source
Molecule: Coagulation Factor Vii
Chain: L
Fragment: Light Chain, Residues 61-212
Ec: 3.4.21.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F7
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Embryonic Kidney Cell Line 293;

Molecule: Coagulation Factor Vii
Chain: H
Fragment: Heavy Chain, Residues 213-466
Ec: 3.4.21.21
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F7
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Embryonic Kidney Cell Line 293;

Molecule: Tissue Factor
Chain: T
Fragment: Residues 34-251
Synonym: Tf, Coagulation Factor III, Thromboplastin, Cd142 Antigen;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Des3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-21a(+)
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.070 68.940 78.730 90.00 90.17 90.00
method X-Ray Diffractionresolution 2.54 Å
ligand N1H BindingDB enzyme Hydrolase E.C.3.4.21.21 BRENDA
Primary referenceDiscovery of novel heterocyclic factor VIIa inhibitors., Rai R, Kolesnikov A, Sprengeler PA, Torkelson S, Ton T, Katz BA, Yu C, Hendrix J, Shrader WD, Stephens R, Cabuslay R, Sanford E, Young WB, Bioorg Med Chem Lett. 2006 Feb 2;. PMID:16460932
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (2f9b.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 2F9B
  • CSU: Contacts of Structural Units for 2F9B
  • Likely Quarternary Molecular Structure file(s) for 2F9B
  • Structure Factors (191 Kb)
  • Retrieve 2F9B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2F9B from S2C, [Save to disk]
  • Re-refined 2f9b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2F9B 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 2F9B
  • 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 2F9B, from MSDmotif at EBI
  • Fold representative 2f9b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2f9b_L] [2f9b_H] [2f9b_T] [2f9b]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 2F9B: [EGF] [EGF_CA] [GLA] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 2F9B with the sequences similar proteins can be viewed for 2F9B's classification [FA7_HUMAN] [TF_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 [FA7_HUMAN] [TF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2F9B
  • Community annotation for 2F9B 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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