2B7D Blood Clotting date Oct 04, 2005
title Factor Viia Inhibitors: Chemical Optimization, Preclinical Pharmacokinetics, Pharmacodynamics, And Efficacy In A Baboon Thrombosis Model
authors W.B.Young, J.Mordenti, S.Torkelson, W.D.Shrader, A.Kolesnikov, R.Rai, L.Liu, H.Hu, E.M.Leahy, M.J.Green, P.A.Sprengeler, B.A.Katz, C.Yu, J.W.Janc, K.C.Elrod, U.M.Marzec, S.R.Hanson
compound source
Molecule: Coagulation Factor Vii
Chain: L
Fragment: Light Chain
Synonym: Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
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: Hek 293
Expression_system_atcc_number: Crl-1573

Molecule: Coagulation Factor Vii
Chain: H
Fragment: Heavy Chain
Synonym: Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
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: Hek 293
Expression_system_atcc_number: Crl-1573

Molecule: Tissue Factor
Chain: T
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
symmetry Space Group: P 1 21 1
R_factor 0.247 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.700 69.030 78.190 90.00 89.49 90.00
method X-Ray Diffractionresolution 2.24 Å
ligand C1B enzyme Hydrolase E.C.3.4.21.21 BRENDA
Primary referenceFactor VIIa inhibitors: Chemical optimization, preclinical pharmacokinetics, pharmacodynamics, and efficacy in an arterial baboon thrombosis model., Young WB, Mordenti J, Torkelson S, Shrader WD, Kolesnikov A, Rai R, Liu L, Hu H, Leahy EM, Green MJ, Sprengeler PA, Katz BA, Yu C, Janc JW, Elrod KC, Marzec UM, Hanson SR, Bioorg Med Chem Lett. 2006 Jan 10;. PMID:16412633
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (2b7d.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 2B7D
  • CSU: Contacts of Structural Units for 2B7D
  • Likely Quarternary Molecular Structure file(s) for 2B7D
  • Structure Factors (286 Kb)
  • Retrieve 2B7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2B7D from S2C, [Save to disk]
  • Re-refined 2b7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2B7D 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 2B7D
  • 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 2B7D, from MSDmotif at EBI
  • Fold representative 2b7d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2b7d_L] [2b7d_T] [2b7d] [2b7d_H]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 2B7D: [EGF] [EGF_CA] [GLA] [Tryp_SPc ] by SMART
  • Other resources with information on 2B7D
  • Community annotation for 2B7D 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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