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PDBsum entry 1tnh
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protein ligands metals links
Hydrolase/hydrolase inhibitor PDB id
1tnh

 

 

 

 

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Contents
Protein chain
223 a.a. *
Ligands
FBA
Metals
_CA
Waters ×489
* Residue conservation analysis
PDB id:
1tnh
Name: Hydrolase/hydrolase inhibitor
Title: Prediction of novel serine protease inhibitors
Structure: Trypsin. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
1.80Å     R-factor:   0.168    
Authors: I.Kurinov,R.W.Harrison
Key ref: I.V.Kurinov and R.W.Harrison (1994). Prediction of new serine proteinase inhibitors. Nat Struct Biol, 1, 735-743. PubMed id: 7634078
Date:
21-Jul-94     Release date:   30-Nov-94    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus
Seq:
Struc: 		246 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.4  - trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

 

 
Nat Struct Biol 1:735-743 (1994)
PubMed id: 7634078  
 
 
Prediction of new serine proteinase inhibitors.
I.V.Kurinov, R.W.Harrison.
 
  ABSTRACT  
 
We describe here the use of a rapid computational method to predict the relative binding strengths of a series of small-molecule ligands for the serine proteinase trypsin. Flexible molecular models of the ligands were docked to the proteinase using an all-atom potential set, without cutoff limits for the non-bonded and electrostatic energies. The binding-strength calculation is done directly in terms of a molecular mechanics potential. The binding of eighteen different compounds, including non-binding controls, has been successfully predicted. The measured Ki is correlated with the predicted energy. The correctness of the theoretical calculations is demonstrated with both kinetics measurements and X-ray structure determination of six enzyme-inhibitor complexes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20101644 V.Zoete, A.Grosdidier, M.Cuendet, and O.Michielin (2010).
Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
  J Mol Recognit, 23, 457-461.  
15529328 A.E.Cho, J.A.Wendel, N.Vaidehi, P.M.Kekenes-Huskey, W.B.Floriano, P.K.Maiti, and W.A.Goddard (2005).
The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals.
  J Comput Chem, 26, 48-71.  
15841474 A.E.Cho, V.Guallar, B.J.Berne, and R.Friesner (2005).
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach.
  J Comput Chem, 26, 915-931.  
16833982 A.Khandelwal, V.Lukacova, D.M.Kroll, S.Raha, D.Comez, and S.Balaz (2005).
Processing multimode binding situations in simulation-based prediction of ligand-macromolecule affinities.
  J Phys Chem A, 109, 6387-6391.  
15578663 O.Guvench, D.J.Price, and C.L.Brooks (2005).
Receptor rigidity and ligand mobility in trypsin-ligand complexes.
  Proteins, 58, 407-417.  
15044735 H.K.Leiros, B.O.Brandsdal, O.A.Andersen, V.Os, I.Leiros, R.Helland, J.Otlewski, N.P.Willassen, and A.O.Smalås (2004).
Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements.
  Protein Sci, 13, 1056-1070.
PDB codes: 1utj 1utk 1utl 1utm 1utn 1uto 1utp 1utq
15470756 M.S.Lee, F.R.Salsbury, and M.A.Olson (2004).
An efficient hybrid explicit/implicit solvent method for biomolecular simulations.
  J Comput Chem, 25, 1967-1978.  
12116383 S.M.Schwarzl, T.B.Tschopp, J.C.Smith, and S.Fischer (2002).
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
  J Comput Chem, 23, 1143-1149.  
10651279 N.Ota, C.Stroupe, J.M.Ferreira-da-Silva, S.A.Shah, M.Mares-Guia, and A.T.Brunger (1999).
Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine.
  Proteins, 37, 641-653.
PDB codes: 1ce5 2bza
10328266 S.M.King, and W.C.Johnson (1999).
Assigning secondary structure from protein coordinate data.
  Proteins, 35, 313-320.  
  9385639 I.T.Weber, and R.W.Harrison (1997).
Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates.
  Protein Sci, 6, 2365-2374.  
  8845765 I.V.Kurinov, and R.W.Harrison (1996).
Two crystal structures of the leupeptin-trypsin complex.
  Protein Sci, 5, 752-758.
PDB codes: 1jrs 1jrt
8728658 P.Bamborough, and F.E.Cohen (1996).
Modeling protein-ligand complexes.
  Curr Opin Struct Biol, 6, 236-241.  
8749843 R.W.Harrison, D.Chatterjee, and I.T.Weber (1995).
Analysis of six protein structures predicted by comparative modeling techniques.
  Proteins, 23, 463-471.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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