1SB1 | pdb_00001sb1

Novel Non-Covalent Thrombin Inhibitors Incorporating P1 4,5,6,7-Tetrahydrobenzothiazole Arginine Side Chain Mimetics

PDB DOI: https://doi.org/10.2210/pdb1SB1/pdb

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

Deposited: 2004-02-09 Released: 2004-06-08
Deposition Author(s): Marinko, P., Krbavcic, A., Mlinsek, G., Solmajer, T., Trampus-Bakija, A., Stegnar, M., Stojan, J., Kikelj, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.224 (Depositor), 0.185 (DCC)
R-Value Work:
0.200 (Depositor), 0.190 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel non-covalent thrombin inhibitors incorporating P(1) 4,5,6,7-tetrahydrobenzothiazole arginine side chain mimetics

Marinko, P., Krbavcic, A., Mlinsek, G., Solmajer, T., Trampus-Bakija, A., Stegnar, M., Stojan, J., Kikelj, D.

(2004) Eur J Med Chem 39: 257-265

PubMed: 15051174 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2003.12.006
Primary Citation Related Structures:
1SB1

PubMed Abstract:
The design, synthesis and biological activity of a series of novel non-covalent D-Phe-Pro-Arg motif-based thrombin inhibitors incorporating 4,5,6,7-tetrahydrobenzothiazol-2-amine as a novel arginine surrogate are described. Compound 9, the most potent in the series of thrombin inhibitors, exhibited an in vitro K(i) of 128 nM and 342-fold selectivity against trypsin. The binding mode of this novel class of thrombin inhibitors in the enzyme active site, based on the X-ray crystal structure of compound 9 co-crystallized with human alpha-thrombin, is discussed.

Organizational Affiliation

Faculty of Pharmacy, University of Ljubljana, Askerceva 7, 1000 Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 34.95 kDa
Atom Count: 2,663
Modeled Residue Count: 288
Deposited Residue Count: 296
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth L]	29	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B [auth H]	258	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hirugen	C [auth I]	9	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28504 (Hirudo medicinalis) Explore P28504 Go to UniProtKB: P28504
Entity Groups
UniProt Group	P28504
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
165 Query on 165 Download:Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	N-(BENZYLSULFONYL)-3-CYCLOHEXYLALANYL-N-(2-AMINO-1,3-BENZOTHIAZOL-6-YL)PROLINAMIDE C₂₈ H₃₅ N₅ O₄ S₂ HDSAIJKTEVRQHF-RPWUZVMVSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H]	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H] Interactions & Density Focus chain D [auth H] Focus chain E [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	C [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224 (Depositor), 0.185 (DCC)
R-Value Work: 0.200 (Depositor), 0.190 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.963	α = 90
b = 71.495	β = 100.15
c = 72.186	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-08
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2011-11-16
Changes: Atomic model
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary