1K1I

BOVINE TRYPSIN-INHIBITOR COMPLEX

PDB DOI: 10.2210/pdb1K1I/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2001-09-25 Released: 2001-11-28
Deposition Author(s): Stubbs, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work: 0.165
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.

Dullweber, F., Stubbs, M.T., Musil, D., Sturzebecher, J., Klebe, G.

(2001) J Mol Biol 313: 593-614

PubMed: 11676542 Search on PubMed
DOI: 10.1006/jmbi.2001.5062
Primary Citation of Related Structures:
1K1I, 1K1J, 1K1L, 1K1M, 1K1N, 1K1O, 1K1P, 1K21, 1K22

PubMed Abstract:

The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur and are overlaid on the binding process. They result from induced pK(a) shifts depending on the local environment experienced by the ligand and protein functional groups in the complex (induced dielectric fit). They involve additional heat effects that must be corrected before any conclusion on the binding enthalpy (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in both contributions can be interpreted in structural terms with respect to the hydrogen bond inventory or residual ligand motions. For all inhibitors studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with increasing temperature. Due to a mutual compensation, Gibbs free energy remains virtually unchanged. The strong negative DeltaC(p) value cannot solely be explained by the removal of hydrophobic surface portions of the protein or ligand from water exposure. Additional contributions must be considered, presumably arising from modulations of the local water structure, changes in vibrational modes or other ordering parameters. For thrombin, smaller negative DeltaC(p) values are observed for ligand binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound water structure.

Related Citations:

Structural and Functional Analyses of Benzamidine-Based Inhibitors in Complex with Trypsin: Implications for the Inhibition of Factor Xa, Tpa, and Urokinase
Renatus, M., Bode, W., Huber, R., Stuerzebecher, J., Stubbs, M.T.
(1998) J Med Chem 41: 5445

Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
Stubbs, M.T., Huber, R., Bode, W.
(1995) FEBS Lett 375: 103

A Player of Many Parts: The Spotlight Falls on Thrombin's Structure
Stubbs, M.T., Bode, W.
(1993) Thromb Res 69: 1

Organizational Affiliation:

Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg (Lahn), Germany.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN	A	223	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FD1 Query on FD1 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	N-ALPHA-(2-NAPHTHYLSULFONYL)-N-(3-AMIDINO-L-PHENYLALANINYL)-D-PIPECOLINIC ACID C₂₆ H₂₈ N₄ O₅ S GNANSBQAIRJZPA-XZOQPEGZSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
FD1	BindingDB: 1K1I	Ki: 1.00e+14 (nM) from 1 assay(s)
	Binding MOAD: 1K1I	Kd: 264 (nM) from 1 assay(s)
	PDBBind: 1K1I	Kd: 264 (nM) from 1 assay(s)