5U6J | pdb_00005u6j

Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide

• PDB DOI: https://doi.org/10.2210/pdb5U6J/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Cricetinae
• Mutation(s): No 


• Deposited: 2016-12-08 Released: 2017-05-10 
• Deposition Author(s): Wei, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.220 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Neutral macrocyclic factor VIIa inhibitors.

Wurtz, N.R., Parkhurst, B.L., DeLucca, I., Glunz, P.W., Jiang, W., Zhang, X., Cheney, D.L., Bozarth, J.M., Rendina, A.R., Wei, A., Harper, T., Luettgen, J.M., Wu, Y., Wong, P.C., Seiffert, D.A., Wexler, R.R., Priestley, E.S.

(2017) Bioorg Med Chem Lett 27: 2650-2654

• PubMed: 28460818 
• DOI: https://doi.org/10.1016/j.bmcl.2017.04.008
• Primary Citation Related Structures: 
  5U6J


• PubMed Abstract: 
  

  Factor VIIa (FVIIa) inhibitors have shown strong antithrombotic efficacy in preclinical thrombosis models with limited bleeding liabilities. Discovery of potent, orally active FVIIa inhibitors has been largely unsuccessful due to the requirement of a basic P1 group to interact with Asp189 in the S1 binding pocket, limiting their membrane permeability. We have combined recently reported neutral P1 binding substituents with a highly optimized macrocyclic chemotype to produce FVIIa inhibitors with low nanomolar potency and enhanced permeability.

---

Organizational Affiliation: 
• Bristol-Myers Squibb Research and Development, Princeton, NJ 08534, United States. Electronic address: [e-mail].
Bristol-Myers Squibb Research and Development, Princeton, NJ 08534, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 35.34 kDa 
• Atom Count: 2,673 
• Modeled Residue Count: 306 
• Deposited Residue Count: 309 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII Heavy Chain	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 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII Light Chain	B [auth L]	55	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
82J	C [auth H]	3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide C31 H36 N4 O6 S KZSYSYPLRUUKEU-MUUNZHRXSA-N
SO4	E [auth H], F [auth H], G [auth H], H	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth H], J [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
82J	BindingDB:  5U6J	Ki: 610 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.220 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.43	α = 90
b = 95.43	β = 90
c = 117.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Wei, A.

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references
• Version 1.2: 2017-06-07
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary