2FES | pdb_00002fes

Orally active thrombin inhibitors

PDB DOI: https://doi.org/10.2210/pdb2FES/pdb

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

Deposited: 2005-12-16 Released: 2006-05-09
Deposition Author(s): Hoeffken, H.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.220 (Depositor)
R-Value Work:
0.170 (Depositor)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Orally active thrombin inhibitors. Part 1: optimization of the P1-moiety.

Mack, H., Baucke, D., Hornberger, W., Lange, U.E.W., Seitz, W., Hoeffken, H.W.

(2006) Bioorg Med Chem Lett 16: 2641-2647

PubMed: 16517159 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.02.040
Primary Citation Related Structures:
2FEQ, 2FES

PubMed Abstract:
The synthesis and SAR of novel nanomolar thrombin inhibitors with the common backbone HOOC-CH(2)-d-cyclohexylalanyl-3,4-dehydroprolyl-NH-CH(2)-aryl-C(=NH)NH(2) are described together with their ecarin clotting time (ECT) prolongation as measure for thrombin inhibition ex vivo. The aryl P1-moiety mimicking the arginine part of the d-Phe-Pro-Arg derived thrombin inhibitors turned out to be a key component for in vitro potency and in vivo activity. Optimization of this part led to compounds with improved antithrombin activity in rats and dogs after oral administration compared to the recently launched anticoagulant melagatran.

Organizational Affiliation

Abbott GmbH & Co. KG, D-67061 Ludwigshafen, Germany. helmut.mack@abbott.com

Macromolecule Content

Total Structure Weight: 35.85 kDa
Atom Count: 2,529
Modeled Residue Count: 292
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B [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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Decapeptide Hirudin Analogue	C [auth D]	11	Hirudo medicinalis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3SP Query on 3SP 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-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({5-[(E)-AMINO(IMINO)METHYL]THIEN-2-YL}METHYL)-L-PROLINAMIDE C₂₂ H₃₃ N₅ O₄ S WWADFOUMUCMPEO-SJORKVTESA-N		Interactions Focus chain D [auth H]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC Query on ALC	C [auth D]	L-PEPTIDE LINKING	C₉ H₁₇ N O₂		ALA
HYP Query on HYP	C [auth D]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO
SMF Query on SMF	C [auth D]	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₅ S		PHE

Binding Affinity Annotations
ID	Source	Binding Affinity
3SP	BindingDB: 2FES	IC50: 1 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000613 (3SP) Query on PRD_000613	D [auth H]	N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-({5-[(E)-amino(imino)methyl]thien-2-yl}methyl)-L-prolinamide	Peptide-like / Thrombin inhibitor		Interactions Focus chain D [auth H]

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000480 Query on PRD_000480	C [auth D]	HIRUDIN ANALOGUE	Oligopeptide / Anticoagulant, Antithrombotic		Interactions Focus chain C [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.220 (Depositor)
R-Value Work: 0.170 (Depositor)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.24	α = 90
b = 72.39	β = 101.01
c = 73.06	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
X-GEN	data reduction
CNX	refinement
SAINT	data reduction
X-GEN	data scaling
CNX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Hoeffken, H.W.

Revision History (Full details and data files)

Version 1.0: 2006-05-09
Type: Initial release
Version 1.1: 2008-05-01
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: 2012-12-12
Changes: Other
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2018-04-04
Changes: Data collection
Version 1.6: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description