2C4F

crystal structure of factor VII.stf complexed with pd0297121

• PDB DOI:  https://doi.org/10.2210/pdb2C4F/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-10-18 Released: 2006-10-18 
• Deposition Author(s): Kohrt, J.T., Zhang, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Work: 0.229 
• R-Value Observed: 0.229 

Literature

The Discovery of Fluoropyridine-Based Inhibitors of the Factor Viia/Tf Complex--Part 2

Kohrt, J.T., Filipski, K.J., Cody, W.L., Cai, C., Dudley, D.A., Huis, C.A.V., Willardsen, J.A., Narasimhan, L.S., Zhang, E., Rapundalo, S.T., Saiya-Cork, K., Leadley, R.J., Edmunds, J.J.

(2006) Bioorg Med Chem Lett 16: 1060

• PubMed: 16289811 
• DOI: https://doi.org/10.1016/j.bmcl.2005.10.076
• Primary Citation of Related Structures:  
  2C4F


• PubMed Abstract: 
  

The activated factor VII/tissue factor complex (FVIIa/TF) is known to play a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. A fluoropyridine-based series of FVIIa/TF inhibitors was discovered which utilized a diisopropylamino group for binding in the S2 and S3 binding pockets of the active site of the enzyme complex. In this series, an enhancement in binding affinity was observed by substitution at the 5-position of the hydroxybenzoic acid sidechain. An X-ray crystal structure indicates that amides at this position may increase inhibitor binding affinity through interactions with the S1'/S2' pocket.

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Organizational Affiliation: 

Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 67.88 kDa 
• Atom Count: 5,058 
• Modelled Residue Count: 584 
• Deposited Residue Count: 587 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR VII PRECURSOR	A [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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR VII PRECURSOR	B [auth L]	142	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE FACTOR PRECURSOR	C [auth T]	75	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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE FACTOR PRECURSOR	D [auth U]	116	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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GIL	F [auth H]	2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BEN ZOIC ACID C30 H35 F2 N5 O5 JLWMMYZWEHHTFF-UHFFFAOYSA-N
NAG	M [auth U]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLC	H [auth L]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
FUC	I [auth L]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA	E [auth H], G [auth L], J [auth L], K [auth L], 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
GIL	Binding MOAD:  2C4F	IC50: 20 (nM) from 1 assay(s)
	BindingDB:  2C4F	IC50: 20 (nM) from 1 assay(s)
	PDBBind:  2C4F	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Work: 0.229 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.993	α = 90
b = 81.302	β = 90
c = 125.86	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-18 
Deposition Author(s): Kohrt, J.T., Zhang, E.

Revision History  

• Version 1.0: 2006-10-18
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Derived calculations
• Version 1.4: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary