Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 71.55 kDa 
• Atom Count: 5091 
• Residue Count: 587 
• Unique protein chains: 3

1WUN

Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-Trp-Gln-p-aminobenzamidine

• DOI: 10.2210/pdb1WUN/pdb

• Classification: HYDROLASE/BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-08 Released: 2005-12-08 
• Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Yoshihashi, K., Kitazawa, T., Suzuki, T., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Ono, Y., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 

Literature

Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor

Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Yoshihashi, K., Kitazawa, T., Suzuki, T., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Ono, Y., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

(2005) Biochem Biophys Res Commun 327: 589-596

• PubMed: 15629154 
• DOI: 10.1016/j.bbrc.2004.12.042
• Primary Citation of Related Structures:  
  1WUN, 1WV7


• PubMed Abstract: 
  

Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is seen as a promising target for developing new anticoagulant drugs. Structure-based designs of the P3 moiety in the peptide mimetic factor VIIa inhibitor successfully lead to novel inhibitors with selectivity for FVIIa/TF and extrinsic coagulation the same as or even higher than those of previously reported peptide mimetic factor VIIa inhibitors. X-ray crystal structure analysis reveals that one of the novel inhibitors shows improved selectivity by forming interactions between the inhibitor and FVIIa as expected. Another of the novel inhibitors achieves improved selectivity through an unexpected hydrogen bond with Gln217, with a unique bent conformation in FVIIa/TF accompanied by conformational changes of the inhibitor and the protein.

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Organizational Affiliation: 

Fuji Gotemba Research Labs, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	L	152	Homo sapiens	Mutation(s): 10  Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	H	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	T	218	Homo sapiens	Mutation(s): 0  Gene Names: F3
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
NIH Common Fund Data Resources
PHAROS:  P13726 GTEx:  ENSG00000117525

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P5B	H	N-(ETHYLSULFONYL)TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLUTAMAMIDE C26 H33 N7 O5 S FJGWLOKDOKYXMU-FCHUYYIVSA-N
BGC	L	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	L	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA	H, L	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	L	L-PEPTIDE LINKING	C6 H9 N O6		GLU

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
P5B	IC50 :  62   nM  PDBBind
P5B	IC50:  69   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.29	α = 90
b = 82.53	β = 90
c = 123.53	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-08 
• Released Date: 2005-12-08 
Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Yoshihashi, K., Kitazawa, T., Suzuki, T., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Ono, Y., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

Revision History 

• Version 1.0: 2005-12-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary