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: 71.59 kDa 
• Atom Count: 5248 
• Modelled Residue Count: 587 
• Deposited Residue Count: 624 
• Unique protein chains: 3

1WTG

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

• DOI: 10.2210/pdb1WTG/pdb

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


• Deposited: 2004-11-23 Released: 2005-11-23 
• Deposition Author(s): Kadono, S., Sakamoto, S., Kikuchi, Y., Oh-Eda, M., Yabuta, N., Kitazawa, K., Yoshihashi, T., Suzuki, T., Koga, T., Hattori, K., Shiraishi, T., Kodama, M., Haramura, 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: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.204 

Literature

Novel interactions of large P3 moiety and small P4 moiety in the binding of 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 326: 859-865

• PubMed: 15607748 
• DOI: 10.1016/j.bbrc.2004.11.108
• Primary Citation of Related Structures:  
  1WTG


• PubMed Abstract: 
  

Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is seen as a promising target for developing new anticoagulant drugs. A novel peptide mimetic factor VIIa inhibitor, ethylsulfonamide-d-biphenylalanine-Gln-p-aminobenzamidine, shows 100-fold selectivity against thrombin in spite of its large P3 moiety, unlike previously reported FVIIa/TF selective inhibitors. X-ray crystal structure analysis reveals that the large P3 moiety, d-biphenylalanine, and the small P4 moiety, ethylsulfonamide, make novel interactions with the 170-loop and Lys192 of FVIIa/TF, respectively, accompanying ligand-induced conformational changes of the 170-loop, Gln217, and Lys192. Structural comparisons of FVIIa with thrombin and amino acid sequence comparisons among coagulation serine proteases suggest that these interactions play an important role in achieving selective inhibition for FVIIa/TF.

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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	A [auth L]	152	Homo sapiens	Mutation(s): 10  Gene Names: F7 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
Coagulation factor VII	B [auth H]	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	Homo sapiens	Mutation(s): 0  Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3BP (Subject of Investigation/LOI)	O [auth H]	2-(3-BIPHENYL-4-YL-2-ETHANESULFONYLAMINO-PROPIONYLAMINO)-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIMIDOYL-BENZYLAMIDE) C30 H36 N6 O5 S DSXLGZNVVMZNSK-IZZNHLLZSA-N
BGC (Subject of Investigation/LOI)	D [auth L]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC (Subject of Investigation/LOI)	E [auth L]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA	F [auth L],  G [auth L],  H [auth L],  I [auth L],  J [auth L],  K [auth L],  L,  M [auth L],  N [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
3BP	Binding MOAD:  1WTG	IC50: 93 (nM) from 1 assay(s)
	PDBBind:  1WTG	IC50: 93 (nM) from 1 assay(s)
	BindingDB:  1WTG	IC50: 93 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.28	α = 90
b = 82.32	β = 90
c = 123.38	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2004-11-23 
• Released Date: 2005-11-23 
Deposition Author(s): Kadono, S., Sakamoto, S., Kikuchi, Y., Oh-Eda, M., Yabuta, N., Kitazawa, K., Yoshihashi, T., Suzuki, T., Koga, T., Hattori, K., Shiraishi, T., Kodama, M., Haramura, H., Ono, Y., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

Revision History  

• Version 1.0: 2005-11-23
  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