1NT1 Blood Clotting Hydrolase Inhibitor date Jan 28, 2003
title Thrombin In Complex With Selective Macrocyclic Inhibitor
authors P.G.Nantermet, J.C.Barrow, C.L.Newton, J.M.Pellicore, M.Young, S. B.J.Lucas, J.A.Krueger, D.R.Mcmasters, Y.Yan, L.C.Kuo, J.P.Vacca H.G.Selnick
compound source
Molecule: Thrombin
Chain: A
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Plasma From Blood

Molecule: Hirudin
Chain: H
Engineered: Yes
Other_details: 10 Aa Hirudin Analogue

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.190 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.100 72.100 73.200 90.00 100.90 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand T76, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1BCU, 1DE7
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDesign and synthesis of potent and selective macrocyclic thrombin inhibitors., Nantermet PG, Barrow JC, Newton CL, Pellicore JM, Young M, Lewis SD, Lucas BJ, Krueger JA, McMasters DR, Yan Y, Kuo LC, Vacca JP, Selnick HG, Bioorg Med Chem Lett 2003 Aug 18;13(16):2781-4. PMID:12873514
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (1nt1.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1NT1
  • CSU: Contacts of Structural Units for 1NT1
  • Likely Quarternary Molecular Structure file(s) for 1NT1
  • Retrieve 1NT1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NT1 from S2C, [Save to disk]
  • View 1NT1 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 1NT1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NT1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nt1a_, region A [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: [1nt1_H] [1nt1] [1nt1_A]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1NT1: [Tryp_SPc ] by SMART
  • Other resources with information on 1NT1
  • Community annotation for 1NT1 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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