Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 71548.39 
• Atom Count: 4734 
• Residue Count: 624 
• 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: Escherichia coli, Homo sapiens


• 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: 2.4 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:  
  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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VII	L	152	Homo sapiens	Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Go to Gene View: F7 Go to UniProtKB:  P08709

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VII	H	254	Homo sapiens	Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Go to Gene View: F7 Go to UniProtKB:  P08709

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Tissue factor	T	218	Homo sapiens	Gene Names: F3
Find proteins for P13726 (Homo sapiens) Go to Gene View: F3 Go to UniProtKB:  P13726

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	H, L	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
BGC	L	BETA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	L	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
P5B	H	N-(ETHYLSULFONYL)TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLUTAMAMIDE 2-[2-ETHANESULFONYLAMINO-3-(1H-INDOL-3-YL)-PROPIONYLAMINO]-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIM IDOYL-BENZYLAMIDE) C26 H33 N7 O5 S FJGWLOKDOKYXMU-FCHUYYIVSA-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: 69 nM BINDINGMOAD
P5B	IC50: 62 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 71.290	α = 90.00
b = 82.530	β = 90.00
c = 123.530	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNX	refinement

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance