1W8B

Factor7 - 413 complex

• PDB DOI: https://doi.org/10.2210/pdb1W8B/pdb

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


• Deposited: 2004-09-17 Released: 2005-10-25 
• Deposition Author(s): Ackermann, J., Alig, L., Banner, D.W., Boehm, H.-J., Groebke-Zbinden, K., Hilpert, K., Lave, T., Kuehne, H., Obst-Sander, U., Riederer, M.A., Stahl, M., Tschopp, T.B., Weber, L., Wessel, H.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Selective and Orally Bioavailable Phenylglycine Tissue Factor/Factor Viia Inhibitors

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.

(2005) Bioorg Med Chem Lett 15: 5344

• PubMed: 16213138 
• DOI: https://doi.org/10.1016/j.bmcl.2005.04.079
• Primary Citation of Related Structures:  
  1W7X, 1W8B


• PubMed Abstract: 
  

  We describe the structure-based design and synthesis of highly potent, orally bioavailable tissue factor/factor VIIa inhibitors which interfere with the coagulation cascade by selective inhibition of the extrinsic pathway.

---

Organizational Affiliation: 

F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.95 kDa 
• Atom Count: 2,434 
• Modelled Residue Count: 303 
• Deposited Residue Count: 311 
• Unique protein chains: 2

Macromolecules

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
GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA	B [auth L]	57	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
GTEx:  ENSG00000057593

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
413	D [auth H]	(S)-[(R)-2-(4-BENZYLOXY-3-METHOXY-PHENYL)-2-(4-CARBAMIMIDOYL-PHENYLAMINO)-ACETYLAMINO]-PHENYL-ACETIC ACID C31 H30 N4 O5 WGEGXJPYFSZDMU-IZLXSDGUSA-N
CA	C [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
413	BindingDB:  1W8B	Ki: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.846	α = 90
b = 82.846	β = 90
c = 147.768	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Ackermann, J., Alig, L., Banner, D.W., Boehm, H.-J., Groebke-Zbinden, K., Hilpert, K., Lave, T., Kuehne, H., Obst-Sander, U., Riederer, M.A., Stahl, M., Tschopp, T.B., Weber, L., Wessel, H.P.

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description