1W0Y

tf7a_3771 complex

• PDB DOI: https://doi.org/10.2210/pdb1W0Y/pdb

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


• Deposited: 2004-05-27 Released: 2005-01-21 
• Deposition Author(s): Banner, D.W., D'Arcy, A., Groebke-Zbinden, K., Ackermann, J., Kirchhofer, D., Ji, Y.-H., Tschopp, T.B., Wallbaum, S., Weber, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.199 

Starting Model: experimental

Literature

Design of Selective Phenylglycine Amide Tissue Factor/Factor Viia Inhibitors

Groebke-Zbinden, K., Banner, D.W., Ackermann, J., D'Arcy, A., Kirchhofer, D., Ji, Y.-H., Tschopp, T.B., Wallbaum, S., Weber, L.

(2005) Bioorg Med Chem Lett 15: 817

• PubMed: 15664864 
• DOI: https://doi.org/10.1016/j.bmcl.2004.10.092
• Primary Citation of Related Structures:  
  1W0Y, 1W2K


• PubMed Abstract: 
  

  Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.

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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 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 69.48 kDa 
• Atom Count: 5,060 
• Modelled Residue Count: 581 
• Deposited Residue Count: 606 
• Unique protein chains: 3

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]	142	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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P08709-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE FACTOR	C [auth T]	210	Homo sapiens	Mutation(s): 0
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
771	D [auth H]	4-(4-BENZYLOXY-2-METHANESULFONYLAMINO-5-METHOXY-BENZYLAMINO)-BENZAMIDINE C23 H26 N4 O4 S CRFICMUDNBIMKL-UHFFFAOYSA-N
BGC	P [auth L]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	G [auth L]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CAC	F [auth H]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA	E [auth H], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], O [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
771	BindingDB:  1W0Y	Ki: 380 (nM) from 1 assay(s)
	PDBBind:  1W0Y	Ki: 380 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.338	α = 90
b = 82.378	β = 90
c = 123.963	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-21 
Deposition Author(s): Banner, D.W., D'Arcy, A., Groebke-Zbinden, K., Ackermann, J., Kirchhofer, D., Ji, Y.-H., Tschopp, T.B., Wallbaum, S., Weber, L.

Revision History  

• Version 1.0: 2005-01-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  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: Advisory, Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary