1W7X

Factor7 - 413 complex

• PDB DOI: https://doi.org/10.2210/pdb1W7X/pdb

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


• Deposited: 2004-09-14 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

Selective and Orally Bioavailable Phenylglycine Tissue Factor/Factor Viia Inhibitors.

Zbinden, K.G., Obst-Sander, U., Hilpert, K., Kuhne, H., Banner, D.W., Bohm, 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.

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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 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 35.28 kDa 
• Atom Count: 3,008 
• Modelled Residue Count: 302 
• Deposited Residue Count: 309 
• 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
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA	B [auth L]	55	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
413	F [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
SO4	G [auth H], H, I [auth H], J [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth H], D [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
413	PDBBind:  1W7X	Ki: 4 (nM) from 1 assay(s)
	BindingDB:  1W7X	Ki: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95	α = 90
b = 95	β = 90
c = 115.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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: 2011-06-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary