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.

doi:10.2210/pdb1mts/pdb

Macromolecule Content

Total Structure Weight: 23822.92
Atom Count: 1664
Residue Count: 223
Unique protein chains: 1

1MTS

FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN

DOI: 10.2210/pdb1MTS/pdb

Classification: SERINE PROTEINASE
Organism(s): Bos taurus

Deposited: 1997-05-16 Released: 1997-08-20
Deposition Author(s): Stubbs, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.9 Å
R-Value Work: 0.179

wwPDB Validation3D Report Full Report

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

Literature

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: 103-107

PubMed: 7498454 Search on PubMed
Primary Citation of Related Structures:
1MTW, 1MTV, 1MTU
Also Cited By: 1QL9, 1QL8, 1QL7, 1QBO, 1QB9

PubMed Abstract:

Crystal structures of DX9065a and a related bisamidino-aryl inhibitor specific for the blood-clotting factor Xa have been solved in complex with bovine beta-trypsin to a resolution of 1.9 A. Each inhibitor exhibits an extended conformation along the active site, in contrast to the compact folded structures observed for thrombin specific inhibitors. Few direct contacts (predominantly in the S1 pocket) are made between trypsin and the inhibitors. Transfer of the inhibitors to the active site of factor Xa suggests a three-site interaction: salt bridge formation at the base of the primary specificity pocket, extensive hydrophobic surface burial and a weak electrostatic interaction between the distal basic component of the inhibitor and an electronegative cavity of factor Xa formed by three backbone carbonyl oxygens. Additivity of these three interactions is the basis for the observed strong inhibition of factor Xa and provides a framework for the design of novel factor Xa inhibitors. A propionic acid group of the inhibitor would clash with the thrombin specific '60-insertion loop', thus conferring selectivity against thrombin.

Related Citations:

The Ornithodorin-Thrombin Crystal Structure, a Key to the Tap Enigma?
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The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 A Resolution. II. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
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(1975) J.Mol.Biol. 98: 693
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(1990) Eur.J.Biochem. 193: 175
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Organizational Affiliation:

Max-Planck Institut für Biochemie, Martinsried bei München, Germany.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRYPSIN	A	223	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB: P00760
Protein Feature View Full Protein Feature View for P00760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
BX3 Query on BX3 Download SDF File Download CCD File	A	(+)-2-[4-[(-1-ACETIMIDOYL-4-PIPERIDINYL)OXY]-3-(7-AMIDINO-2-NAPHTHYL)PROPIONIC ACID BX5633 C₂₇ H₃₀ N₄ O₃ FZLDAJVXFYWRCX-ISAGNRBTSA-N		Ligand Interaction
CA Query on CA Download SDF File Download CCD File	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction