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: 71.70 kDa 
• Atom Count: 5107 
• Residue Count: 587 
• Unique protein chains: 3

2ZZU

Human Factor VIIA-Tissue Factor Complexed with ethylsulfonamide-D-5-(3-carboxybenzyloxy)-Trp-Gln-p-aminobenzamidine

• DOI: 10.2210/pdb2ZZU/pdb

• Classification: HYDROLASE/BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-25 Released: 2009-03-24 
• Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-Eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Sato, H., Ohta, M., Kozono, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.221 

Literature

Design and synthesis of peptidomimetic factor VIIa inhibitors

Shiraishi, T., Kadono, S., Haramura, M., Kodama, H., Ono, Y., Iikura, H., Esaki, T., Koga, T., Hattori, K., Watanabe, Y., Sakamoto, A., Yoshihashi, K., Kitazawa, T., Esaki, K., Ohta, M., Sato, H., Kozono, T.

(2010) Chem Pharm Bull (Tokyo) 58: 38-44

• PubMed: 20045964 
• DOI: 10.1248/cpb.58.38
• Primary Citation of Related Structures:  
  2ZZU


• PubMed Abstract: 
  

Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is regarded as a promising target for developing new anticoagulant drugs. In previous reports, we described a S3 subsite found in the X-ray crystal structure of compound 2 that bound to FVIIa/soluble tissue factor (sTF). Based on the X-ray crystal structure information and with the aim of improving the inhibition activity for FVIIa/TF and selectivity against other serine proteases, we synthesized derivatives by introducing substituents at position 5 of the indole ring of compound 2. Among them, compound 16 showed high selectivity against other serine proteases. Contrary to our expectations, compound 16 did not occupy the S3-subsite; X-ray structure analysis revealed that compound 16 improved selectivity by forming hydrogen bonds with Gln217, Thr99 and Asn100.

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Organizational Affiliation: 

Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co., Ltd., Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor VII light chain	L	152	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor VII heavy chain	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
359	H	3-[[3-[(2R)-3-[[(2S)-5-amino-1-[(4-carbamimidoylphenyl)methylamino]-1,5-dioxo-pentan-2-yl]amino]-2-(ethylsulfonylamino)-3-oxo-propyl]-1H-indol-5-yl]oxymethyl]benzoic acid C34 H39 N7 O8 S UDNWHSWDIIAZDA-URLMMPGGSA-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 %)
359	IC50 :  39   nM  PDBBind
359	IC50:  39   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.4	α = 90
b = 82.22	β = 90
c = 123.47	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-25 
• Released Date: 2009-03-24 
Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-Eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Sato, H., Ohta, M., Kozono, T.

Revision History 

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-30
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary