7KME

CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2711.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of thrombin retro-inhibited with SEL2711 and SEL2770 as they relate to factor Xa binding.

Mochalkin, I.Tulinsky, A.

(1999) Acta Crystallogr.,Sect.D 55: 785-793

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most thrombin active-site inhibitors form a short antiparallel beta-strand with residues Ser214-Gly216. However, the Selectide Corp. inhibitors SEL2711 and SEL2770 bind to thrombin in a retro fashion, making a parallel beta-strand with Ser214-Gly216 ...

    Most thrombin active-site inhibitors form a short antiparallel beta-strand with residues Ser214-Gly216. However, the Selectide Corp. inhibitors SEL2711 and SEL2770 bind to thrombin in a retro fashion, making a parallel beta-strand with Ser214-Gly216 similar to other retro-binding inhibitors. The crystallographic structures of thrombin-hirugen complexed with SEL2711 and SEL2770, which are isostructural with the binary thrombin-hirugen complex, have been determined and refined in the 9.0-2.1 A resolution range to final R values of 16.5 and 16.7%, respectively. The structures of the SEL2711 and SEL2770 complexes contain 131 and 104 water molecules, respectively, both of which correspond to occupancies of greater than 0.5. The L-4-amidinophenylalanyl residues of SEL2711 and SEL2770 are fixed at the S1 specificity site, utilizing favorable ionic and hydrogen-bonding interactions between the N atoms of the amidino group and the side-chain O atoms of Asp189. The Glu192 residue of thrombin adopts an extended conformation, which allows the L-cyclohexylglycyl residue in the P2 retro-binding position of the inhibitors to occupy a similar site to the P3 aspartate in thrombin platelet-receptor peptides bound to thrombin. The N-terminal acetyl group of both inhibitors is located in the S2 subsite, while the L-3-pyridyl-(3-methyl)-alanyl of SEL2711 and the L-(N,N-dimethyl)lysine of SEL2770 occupy the S3 D-Phe subsite of D-PheProArg chloromethyl ketone (PPACK) in the thrombin-PPACK complex. The two C-terminal residues of SEL2711 (leucine and proline) point into the solvent and have no electron density in the thrombin complex. Those of SEL2770 are also positioned into the solvent, but surprisingly produce weak electron density with high B values ( = 50 A2). Since the Selectide inhibitors are about 10(4) times more specific for factor Xa, modeling retro-binding to the latter suggests that the selectivity can be a consequence of interactions of the inhibitors in the S3-S4 binding subsites of factor Xa.


    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN L-CHAIN
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THROMBIN H-CHAIN
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIRUGEN
I
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SEL2711
J
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.050α = 90.00
b = 71.820β = 101.20
c = 73.450γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-09
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-10-04
    Type: Refinement description