2BZ6

Orally available Factor7a inhibitor

PDB DOI: https://doi.org/10.2210/pdb2BZ6/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-08-11 Released: 2006-02-22
Deposition Author(s): Groebke-Zbinden, K., Obst-Sander, U., Hilpert, K., Kuehne, H., Banner, D.W., Boehm, H.J., Stahl, M., Ackermann, J., Alig, L., Weber, L., Wessel, H.P., Riederer, M.A., Tschopp, T.B., Lave, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.193 (Depositor), 0.192 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Dose-Dependant Antithrombotic Activity of an Orally Active Tissue Factor/Factor Viia Inhibitor without Concomitant Enhancement of Bleeding Propensity.

Groebke-Zbinden, K., Banner, D.W., Hilpert, K., Himber, J., Lave, T., Riederer, M.A., Stahl, M., Tschopp, T.B., Obst-Sander, U.

(2006) Bioorg Med Chem 14: 5357

PubMed: 16621574 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2006.03.042
Primary Citation of Related Structures:
2BZ6

PubMed Abstract:
The discovery of a highly potent and selective tissue factor/factor VIIa inhibitor is described. Upon oral administration of its double prodrug in the guinea pig, a dose-dependent antithrombotic effect is observed in an established model of arterial thrombosis without prolonging bleeding time. The pharmacodynamic properties of this selective inhibitor are compared to the behaviour of a mixed factor VIIa/factor Xa inhibitor.

Organizational Affiliation

F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland. katrin.groebke_zbinden@roche.com

Macromolecule Content

Total Structure Weight: 34.4 kDa
Atom Count: 2,985
Modelled Residue Count: 307
Deposited Residue Count: 307
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA	A [auth H]	254	Homo sapiens	Mutation(s): 0 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA	B [auth L]	53	Homo sapiens	Mutation(s): 0 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
346 Query on 346 Download Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	(R)-(4-CARBAMIMIDOYL-PHENYLAMINO)-[5-ETHOXY-2-FLUORO-3-[(R)-TETRAHYDRO-FURAN-3-YLOXY]-PHENYL]-ACETIC ACID C₂₁ H₂₄ F N₃ O₅ PGYOHIAQCFZQDK-AUUYWEPGSA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
346	BindingDB: 2BZ6	Ki: min: 81, max: 88 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.193 (Depositor), 0.192 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.93	α = 90
b = 94.93	β = 90
c = 115.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-02-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary