2C8Z Hydrolase Hydrolase Inhibitor date Dec 08, 2005
title Thrombin Inhibitors
authors N.Howard, C.Abell, W.Blakemore, R.Carr, G.Chessari, M.Congreve, S. H.Jhoti, C.W.Murray, L.C.A.Seavers, R.L.M.Van Montfort
compound source
Molecule: Thrombin, Light Chain
Chain: A
Fragment: Fragment Alpha Thrombin, Residues 328-363
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Thrombin Heavy Chain
Chain: B
Fragment: Fragment Alpha Thrombin, Residues 364-622
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Hirudin Variant-2
Chain: I
Fragment: Peptide Fragment Of Hirugen, Residues 61-72
Synonym: Hirugen

Organism_scientific: Hirudo Medicinalis
Organism_common: Medicinal Leech
Organism_taxid: 6421
symmetry Space Group: C 1 2 1
R_factor 0.176 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.938 71.657 71.839 90.00 100.10 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand C2A, DMS, NA, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceApplication of fragment screening and fragment linking to the discovery of novel thrombin inhibitors., Howard N, Abell C, Blakemore W, Chessari G, Congreve M, Howard S, Jhoti H, Murray CW, Seavers LC, van Montfort RL, J Med Chem. 2006 Feb 23;49(4):1346-55. PMID:16480269
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2c8z.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 2C8Z
  • CSU: Contacts of Structural Units for 2C8Z
  • Likely Quarternary Molecular Structure file(s) for 2C8Z
  • Structure Factors (139 Kb)
  • Retrieve 2C8Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C8Z from S2C, [Save to disk]
  • Re-refined 2c8z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2C8Z 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 2C8Z
  • 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
  • 3D motif for 2C8Z, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c8z_I] [2c8z_A] [2c8z] [2c8z_B]
  • SWISS-PROT database: [P09945] [P00734]
  • Domain organization of [HIRV2_HIRME] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 2C8Z: [Tryp_SPc ] by SMART
  • Other resources with information on 2C8Z
  • Community annotation for 2C8Z 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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