1MU8 Hydrolase Hydrolase Inhibitor date Sep 23, 2002
title Thrombin-Hirugen_l-378,650
authors C.S.Burgey, K.A.Robinson, T.A.Lyle, P.E.Sanderson, S.D.Lewis, B.J J.A.Krueger, R.Singh, C.Miller-Stein, R.B.White, B.Wong, E.A.Lyl P.D.Williams, C.A.Coburn, B.D.Dorsey, J.C.Barrow, M.T.Stranieri M.A.Holahan, G.R.Sitko, J.J.Cook, D.R.Mcmasters, C.M.Mcdonough, W.M.Sanders, A.A.Wallace, F.C.Clayton, D.Bohn, Y.M.Leonard, T.J. Jr., J.J.Lynch Jr., Y.Yan, Z.Chen, L.Kuo, S.J.Gardell, J.A.Shafer J.P.J.Vacca
compound source
Molecule: Thrombin
Chain: A
Fragment: Light Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Plasma

Molecule: Thrombin
Chain: B
Fragment: Heavy Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5

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

Molecule: Hirudin Iib
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Hirudo Medicinalis
Organism_taxid: 6421
Other_details: This Peptide Was Chemically Synthesized. It Naturally Found In Hirudo Medicinalis (Medicinal Leech).
symmetry Space Group: C 1 2 1
R_factor 0.240 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.120 72.230 73.030 90.00 100.80 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CDB, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1T4U, 1WAY
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceMetabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines., Burgey CS, Robinson KA, Lyle TA, Sanderson PE, Lewis SD, Lucas BJ, Krueger JA, Singh R, Miller-Stein C, White RB, Wong B, Lyle EA, Williams PD, Coburn CA, Dorsey BD, Barrow JC, Stranieri MT, Holahan MA, Sitko GR, Cook JJ, McMasters DR, McDonough CM, Sanders WM, Wallace AA, Clayton FC, Bohn D, Leonard YM, Detwiler TJ Jr, Lynch JJ Jr, Yan Y, Chen Z, Kuo L, Gardell SJ, Shafer JA, Vacca JP, J Med Chem 2003 Feb 13;46(4):461-73. PMID:12570369
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (1mu8.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 1MU8
  • CSU: Contacts of Structural Units for 1MU8
  • Likely Quarternary Molecular Structure file(s) for 1MU8
  • Retrieve 1MU8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MU8 from S2C, [Save to disk]
  • View 1MU8 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 1MU8
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1MU8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1mu8.1, region A:,B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1mu8] [1mu8_B] [1mu8_C] [1mu8_A]
  • SWISS-PROT database: [P28506] [P00734]
  • Domain organization of [HIR2B_HIRME] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1MU8: [Tryp_SPc ] by SMART
  • Other resources with information on 1MU8
  • Community annotation for 1MU8 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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