1W7G | pdb_00001w7g

Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template inhibitor CS107

PDB DOI: https://doi.org/10.2210/pdb1W7G/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2004-09-02 Released: 2006-05-24
Deposition Author(s): Remiche, J., Sauvage, E., Herman, R., Charlier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.272 (Depositor), 0.265 (DCC)
R-Value Work:
0.243 (Depositor), 0.236 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Design, Synthesis and Evaluation of Graftable Thrombin Inhibitors for the Preparation of Blood-Compatible Polymer Materials.

Salvagnini, C., Michaux, C., Remiche, J., Wouters, J., Charlier, P., Marchand-Brynaert, J.

(2005) Org Biomol Chem 3: 4209

PubMed: 16294249 Search on PubMed
DOI: https://doi.org/10.1039/b510239a
Primary Citation Related Structures:
1W7G

PubMed Abstract:
Piperazinyl-amide derivatives of N-alpha-(3-trifluoromethyl-benzenesulfonyl)-L-arginine (1) were synthesized as graftable thrombin inhibitors. The possible disturbance of biological activity due to a variable spacer-arm fixed on the N-4 piperazinyl position was evaluated in vitro, against human alpha-thrombin, and in blood coagulation assay. Molecular modelling (in silico analysis) and X-ray diffraction studies of thrombin-inhibitor complexes were also performed. The fixation of bioactive molecules on poly(butylene terephthalate) (PBT) and poly(ethylene terephthalate) (PET) membranes was performed by wet chemistry treatment and evaluated by XPS analysis. Surface grafting of inhibitor 1d improved the membrane hemocompatibility by reducing blood clot formation on the modified surface.

Organizational Affiliation

Unité de Chimie Organique et Médicinale, Université catholique de Louvain, Bâtiment Lavoisier, place Louis Pasteur 1, B-1348, Louvain-la-Neuve, Belgium.

Macromolecule Content

Total Structure Weight: 35.91 kDa
Atom Count: 2,554
Modeled Residue Count: 289
Deposited Residue Count: 307
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	A [auth H]	259	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN I	B [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	C [auth L]	36	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MIU Query on MIU Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	N-{(1S)-1-{[4-(3-AMINOPROPYL)PIPERAZIN-1-YL]CARBONYL}-4-[(DIAMINOMETHYLENE)AMINO]BUTYL}-3-(TRIFLUOROMETHYL)BENZENESULFONAMIDE C₂₀ H₃₂ F₃ N₇ O₃ S KGJKWHCPJPBEJP-KRWDZBQOSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.272 (Depositor), 0.265 (DCC)
R-Value Work: 0.243 (Depositor), 0.236 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.51	α = 90
b = 71.343	β = 100.59
c = 72.555	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-05-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-05-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary